Contacts of the helix formed by residues 101 - 122 (chain C) in PDB entry 4YC6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C TYR 3.4 5.6 + - - +
100C MET* 1.3 69.9 - - - +
102C SER* 1.3 56.3 + - - +
103C SER* 2.6 30.8 + - - -
104C LEU* 2.6 39.7 + - + +
105C VAL 3.1 8.7 + - - -
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C MET 3.1 7.4 + - - -
101C ASP* 1.3 73.5 - - - +
103C SER* 1.3 59.0 + - - +
105C VAL* 3.4 12.5 - - - +
106C LYS* 3.3 26.7 + - - +
255C ASN* 4.6 20.9 - - - -
256C LEU* 6.3 0.4 - - - -
286C TYR* 3.9 4.8 + - - -
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Residues in contact with SER 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASP* 2.6 23.2 + - - -
102C SER* 1.3 81.5 + - - +
104C LEU* 1.3 60.3 + - - +
106C LYS* 3.7 11.9 - - - +
107C SER* 3.0 25.3 + - - -
289C ASP* 5.9 5.6 - - - -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.8 22.2 - - + +
100C MET* 4.1 14.4 - - + -
101C ASP* 2.6 30.6 + - + +
103C SER* 1.3 74.6 + - - +
105C VAL* 1.3 57.9 + - - +
107C SER* 4.1 9.2 - - - +
108C TYR* 2.8 69.2 + - + +
140C GLY 5.9 0.7 - - - +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C MET* 3.8 34.9 - - - +
101C ASP 3.1 10.2 + - - +
102C SER* 3.4 12.6 - - - +
104C LEU* 1.3 75.1 - - - +
106C LYS* 1.3 53.9 + - - +
108C TYR* 3.0 5.6 + - - +
109C LEU* 2.8 34.3 + - - +
194C PHE* 3.7 23.1 - - + -
197C LEU* 3.8 27.0 - - + +
198C ALA* 4.5 7.2 - - - +
255C ASN 6.0 1.1 - - - +
256C LEU* 4.7 6.7 - - + -
286C TYR* 3.4 15.0 - - - +
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Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C SER 3.3 12.4 + - - +
103C SER* 3.7 11.4 - - - +
104C LEU 3.3 0.2 - - - -
105C VAL* 1.3 76.9 - - - +
107C SER* 1.3 68.7 + - - +
109C LEU* 3.4 0.6 + - - -
110C TYR* 3.2 17.8 + - - +
257C ASP* 4.6 11.7 + - - -
286C TYR* 2.8 67.6 + - + +
287C PHE* 3.5 24.7 - - + -
289C ASP* 2.5 46.8 + - - +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C SER 3.0 16.5 + - - -
104C LEU* 3.4 18.0 - - - +
106C LYS* 1.3 77.5 - - - +
108C TYR* 1.3 67.1 + - - +
110C TYR* 3.2 5.4 + - - +
111C GLN* 2.6 48.7 + - - +
140C GLY 5.2 0.5 + - - -
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Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.9 29.4 - - + -
90C TYR* 4.7 10.8 - + - -
100C MET* 4.2 11.7 - - + -
104C LEU* 2.8 53.4 + - + +
105C VAL 3.5 3.8 - - - +
107C SER* 1.3 74.0 + - - +
109C LEU* 1.3 65.0 + - - +
111C GLN* 3.2 14.5 + - - +
112C ILE* 2.9 33.0 + - + +
136C ILE* 3.6 27.2 - - + +
140C GLY* 4.1 22.0 + - - -
142C ILE* 3.9 18.1 - - + +
197C LEU* 4.2 20.0 - - + -
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C VAL 2.8 19.1 + - - +
106C LYS* 3.8 5.4 - - - +
108C TYR* 1.3 74.5 - - - +
110C TYR* 1.3 51.9 + - - +
112C ILE* 3.2 12.0 + - + +
113C LEU* 2.7 37.0 + - + +
190C ILE* 3.6 32.1 - - + +
194C PHE* 3.6 57.4 - - + -
197C LEU* 4.7 4.0 - - + +
263C LEU* 3.9 9.2 - - + -
267C MET* 4.1 7.0 - - + -
286C TYR* 4.1 2.2 - - + -
287C PHE* 3.7 22.2 - - + -
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS 3.2 10.5 + - - +
107C SER* 3.2 10.1 + - - +
109C LEU* 1.3 78.5 - - - +
111C GLN* 1.3 61.9 + - + +
113C LEU* 3.3 5.1 + - - +
114C GLN* 2.8 66.6 + - - +
282C LEU* 3.4 39.8 + - + +
287C PHE* 3.5 36.2 - + + -
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ASN* 3.3 36.4 - - - +
107C SER* 2.6 35.7 + - - +
108C TYR* 3.5 8.4 - - - +
110C TYR* 1.3 80.7 - - + +
112C ILE* 1.3 62.1 + - - +
114C GLN* 3.3 6.6 + - - +
115C GLY* 3.1 18.2 + - - -
140C GLY 3.8 6.0 + - - +
141C THR* 3.5 14.1 + - - +
142C ILE* 3.2 43.3 - - + +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 5.5 0.9 - - + -
108C TYR* 2.9 29.9 + - + +
109C LEU* 3.5 11.4 - - + +
111C GLN* 1.3 72.8 - - - +
113C LEU* 1.3 65.5 + - - +
115C GLY* 3.3 2.4 + - - -
116C ILE* 3.1 21.3 + - - +
129C LEU* 5.1 2.0 - - + -
134C LEU* 3.6 35.7 - - + -
142C ILE* 4.0 22.4 - - + -
144C LEU* 4.2 19.6 - - + +
190C ILE* 4.0 33.9 - - + -
193C ILE* 5.1 3.8 - - + -
197C LEU* 4.6 11.4 - - + -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 2.7 23.6 + - + +
110C TYR 3.5 4.5 - - - +
112C ILE* 1.3 72.2 - - - +
114C GLN* 1.3 58.3 + - - +
116C ILE* 3.2 7.1 - - + +
117C VAL* 2.9 34.4 + - - +
187C ILE* 4.8 3.6 - - + -
190C ILE* 4.3 15.7 - - + -
267C MET* 4.0 27.4 - - + -
278C GLY* 4.1 15.3 - - - +
281C ALA* 3.8 32.1 - - + -
282C LEU* 3.9 14.1 - - + +
287C PHE* 3.9 29.8 - - + -
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Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C HIS* 3.8 15.0 + - + +
62C ASN* 3.7 17.1 + - - +
110C TYR* 2.8 49.6 + - - +
111C GLN* 3.3 10.5 + - - +
113C LEU* 1.3 73.4 - - - +
115C GLY* 1.3 57.3 + - - +
117C VAL* 3.5 6.5 + - - +
118C PHE* 3.0 28.9 + - - +
282C LEU* 3.9 18.8 - - + -
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C HIS* 4.2 4.5 - - - -
62C ASN* 3.7 27.0 - - - +
63C ILE* 3.8 8.6 - - - +
111C GLN 3.1 10.5 + - - -
112C ILE 3.3 3.3 + - - -
113C LEU 3.3 0.2 - - - -
114C GLN* 1.3 77.1 - - - +
116C ILE* 1.3 57.2 + - - +
118C PHE* 3.5 2.9 - - - +
119C CYS* 3.1 32.6 + - - -
144C LEU* 4.3 5.4 - - - -
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Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ILE 3.1 11.9 + - - +
113C LEU* 3.2 21.5 - - + +
115C GLY* 1.3 75.4 - - - +
117C VAL* 1.3 62.7 + - + +
118C PHE 3.2 0.2 - - - -
119C CYS* 3.0 11.6 + - + +
120C HIS* 2.7 61.9 + - + +
126C HIS* 4.5 9.4 - - + +
129C LEU* 4.9 4.9 - - + -
144C LEU* 3.8 20.6 - - + +
186C ASP* 3.5 32.3 - - + +
187C ILE* 4.4 9.6 - - + -
190C ILE* 3.7 24.0 - - + -
278C GLY* 4.8 0.4 - - - -
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU 2.9 20.0 + - - +
114C GLN* 3.8 3.8 - - - +
116C ILE* 1.3 77.8 - - - +
118C PHE* 1.3 51.0 + - - +
120C HIS* 3.2 9.4 + - - +
121C SER* 2.5 36.8 + - - -
278C GLY* 3.3 42.2 - - - +
279C LYS* 3.5 26.8 - - + +
282C LEU* 3.7 15.9 - - + -
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Residues in contact with PHE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 3.9 28.7 - - + -
59C ARG 3.1 30.5 - - - -
60C HIS* 3.4 38.6 - + + -
63C ILE* 4.1 11.0 - - + -
114C GLN 3.0 12.8 + - - +
115C GLY 3.5 7.0 - - - +
117C VAL* 1.3 77.4 - - - +
119C CYS* 1.3 63.9 - - - +
121C SER* 2.9 22.4 + - - -
122C ARG* 3.2 50.2 + - - +
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Residues in contact with CYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 5.1 3.6 - - - -
63C ILE* 4.1 17.0 - - - -
115C GLY 3.1 19.7 + - - +
116C ILE* 3.0 15.6 + - + +
118C PHE* 1.3 86.2 - - - +
120C HIS* 1.3 59.4 + - + +
122C ARG* 3.1 10.6 + - - -
124C VAL* 2.9 46.2 + - + +
125C LEU* 5.5 1.1 - - - -
144C LEU* 4.8 5.8 - - - -
147C PHE* 4.1 31.4 - - + -
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Residues in contact with HIS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ILE* 2.7 40.9 + - + +
117C VAL* 3.2 7.6 + - - +
118C PHE 3.2 2.4 - - - -
119C CYS* 1.3 74.1 - - - +
121C SER* 1.3 53.0 + - - +
122C ARG 3.2 0.2 - - - -
123C ARG* 2.8 28.8 + - - -
124C VAL 3.4 18.7 + - - -
125C LEU* 3.9 2.7 - - + +
183C THR* 3.2 57.3 - - + +
186C ASP* 3.1 25.7 + - + +
187C ILE* 4.2 12.9 - - + +
278C GLY* 5.4 4.2 + - - -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C VAL* 2.5 34.7 + - - -
118C PHE* 2.9 17.3 + - - -
120C HIS* 1.3 64.2 + - - +
122C ARG* 1.3 72.3 + - - +
123C ARG* 3.3 3.1 + - - +
279C LYS* 5.6 11.4 - - - +
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 4.3 19.3 - - + +
118C PHE* 3.3 56.4 + - - +
119C CYS* 3.1 12.9 + - - +
121C SER* 1.3 101.6 + - - +
123C ARG* 1.3 70.2 + - - +
124C VAL* 3.2 16.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il