Contacts of the helix formed by residues 103 - 118 (chain C) in PDB entry 5L5E
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 THR 103 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C HIS* 5.3 0.2 - - - -
94C HIS* 5.4 0.8 - - - -
101C PRO 3.7 2.6 + - - +
102C VAL* 1.3 80.9 - - - +
104C VAL* 1.3 65.5 + - - +
105C GLU* 3.9 9.1 + - - +
106C TYR* 3.1 28.0 + - - +
107C LEU* 3.1 20.1 + - - +
137C ASP* 3.4 30.5 - - + +
138C PRO* 4.7 5.2 - - + -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 4.4 15.3 - - + -
102C VAL 4.0 0.2 + - - -
103C THR* 1.3 72.3 - - - +
105C GLU* 1.3 58.6 + - - +
107C LEU* 3.5 5.9 + - - +
108C THR* 2.8 33.5 + - - -
133C ILE* 3.9 27.1 - - + +
134C ALA 4.2 5.2 - - - -
135C GLY* 3.6 34.8 - - - +
136C PHE 3.9 5.2 - - - +
137C ASP* 2.9 18.9 + - - +
144C LYS* 3.8 21.8 - - + -
146C TYR* 3.9 13.9 - - + -
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Residues in contact with GLU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C THR* 3.2 8.6 + - - +
104C VAL* 1.3 79.2 - - - +
106C TYR* 1.3 55.8 + - - +
108C THR* 3.4 3.9 + - - -
109C ARG* 2.9 55.6 + - - +
137C ASP* 4.6 1.7 + - - +
144C LYS* 5.8 1.7 - - + +
146C TYR* 3.1 41.6 - - + +
154C TYR* 3.4 24.9 + - + -
57D GLU* 5.2 3.8 - - - +
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Residues in contact with TYR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 2.9 34.7 + - + -
94C HIS* 3.8 28.5 - + - +
102C VAL* 3.7 20.6 - - + -
103C THR* 3.1 26.4 + - - +
105C GLU* 1.3 75.1 + - - +
107C LEU* 1.3 63.6 + - - +
109C ARG* 3.2 40.0 + - - +
110C TYR* 2.9 31.2 + + + +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.9 30.5 - - + -
69C VAL* 4.6 7.0 - - + -
71C LEU* 5.0 0.9 - - + -
87C ALA* 3.8 29.6 - - + +
90C GLU* 5.2 2.7 - - + -
91C ALA* 4.9 4.0 - - + +
102C VAL* 4.0 21.8 - - + -
103C THR 3.1 16.4 + - - +
104C VAL* 3.8 6.7 - - - +
106C TYR* 1.3 79.7 - - - +
108C THR* 1.3 63.1 + - - +
110C TYR* 3.2 10.7 + - + +
111C VAL* 3.0 40.9 + - + +
133C ILE* 4.0 22.4 - - + -
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Residues in contact with THR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL 2.8 22.2 + - - -
105C GLU* 3.6 5.2 - - - -
107C LEU* 1.3 76.9 - - - +
109C ARG* 1.3 57.3 + - - +
111C VAL* 3.3 1.6 + - - +
112C ALA* 2.9 32.9 + - - +
133C ILE* 3.6 23.0 - - + +
146C TYR* 3.4 36.9 - - + +
148C THR* 3.6 22.2 - - + +
154C TYR* 3.7 20.0 - - + -
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C THR* 5.4 0.2 + - - -
105C GLU* 2.9 45.8 + - - +
106C TYR* 3.2 44.1 + - - +
108C THR* 1.3 75.7 - - - +
110C TYR* 1.3 57.5 + - - +
112C ALA* 3.9 1.4 - - - +
113C GLY* 3.0 23.6 + - - -
154C TYR* 3.4 32.6 + - + +
78D ARG* 5.9 6.1 - - + +
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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
----------------------------------------------------------
86C LYS* 3.6 42.8 + - + +
87C ALA* 4.1 8.1 - - - -
89C VAL* 6.2 0.2 - - - +
90C GLU* 3.6 43.2 + - + +
106C TYR* 2.9 19.7 + - + +
107C LEU* 3.5 10.8 - - + +
108C THR 3.2 0.2 - - - -
109C ARG* 1.3 74.8 - - - +
111C VAL* 1.3 72.4 + - + +
113C GLY* 3.1 3.7 + - - -
114C VAL* 3.0 42.9 + - + +
117C ARG* 5.0 9.1 + - - -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.6 5.4 - - + -
83C LEU* 4.3 27.4 - - + +
87C ALA* 3.9 28.5 - - + -
107C LEU* 3.0 26.6 + - + +
108C THR 3.9 2.9 - - - +
110C TYR* 1.3 81.5 - - + +
112C ALA* 1.3 64.1 + - - +
114C VAL* 3.3 8.9 + - - +
115C GLN* 3.1 33.1 + - - +
131C THR* 4.5 5.8 - - + +
133C ILE* 4.3 13.5 - - + -
148C THR* 4.5 7.6 - - - +
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR 2.9 18.2 + - - +
109C ARG 3.9 2.9 - - - +
111C VAL* 1.3 77.7 - - - +
113C GLY* 1.3 58.0 + - - +
115C GLN* 3.3 11.4 + - - +
116C GLN* 3.0 24.4 + - - +
148C THR* 4.1 6.2 - - + +
152C GLY* 3.4 31.0 - - - +
154C TYR* 3.8 27.1 - - + -
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG 3.0 16.7 + - - -
110C TYR* 3.1 4.9 + - - -
112C ALA* 1.3 74.5 - - - +
114C VAL* 1.3 58.8 + - - +
116C GLN* 3.4 8.3 + - - +
117C ARG* 3.0 32.4 + - - +
78D ARG* 6.5 1.3 - - - -
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.7 22.4 - - + -
86C LYS* 3.9 22.9 - - + -
110C TYR* 3.0 45.4 + - + +
111C VAL* 3.3 9.2 + - - +
113C GLY* 1.3 76.1 - - - +
115C GLN* 1.3 62.4 + - - +
117C ARG* 3.3 27.5 + - - +
118C TYR* 3.3 31.4 + - + -
127C PHE* 3.9 10.8 - - + -
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 4.1 27.4 - - + +
111C VAL* 3.1 21.6 + - - +
112C ALA* 3.6 8.6 - - - +
114C VAL* 1.3 76.1 - - - +
116C GLN* 1.3 60.5 + - - +
118C TYR* 3.4 12.5 + - - +
119C THR* 3.4 7.4 + - - +
127C PHE* 4.1 17.4 + - + +
129C VAL 2.9 29.9 + - - -
131C THR* 4.9 0.8 - - - +
148C THR* 2.8 34.4 + - - -
149C GLU 3.5 20.5 - - - +
150C PRO* 3.4 24.2 - - - +
152C GLY* 4.3 0.2 - - - -
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Residues in contact with GLN 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 ALA 3.0 17.2 + - - +
113C GLY* 3.7 8.7 + - - +
114C VAL 3.3 0.2 - - - -
115C GLN* 1.3 72.5 - - - +
117C ARG* 1.3 65.4 + - - +
119C THR* 2.5 35.4 + - - +
120C GLN* 2.8 35.6 + - - +
151C SER 3.7 22.4 - - - +
152C GLY* 4.0 3.7 - - - +
75D ALA* 3.5 30.6 + - + +
76D ASP* 3.0 15.5 - - - +
78D ARG* 6.1 0.6 - - - +
79D SER* 4.9 11.3 + - - +
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Residues in contact with ARG 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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86C LYS* 4.7 13.1 - - - +
110C TYR* 5.0 9.9 + - - -
113C GLY 3.0 17.2 + - - +
114C VAL* 3.3 34.6 + - - +
116C GLN* 1.3 83.5 - - - +
118C TYR* 1.3 75.6 + - + +
119C THR 3.3 0.5 + - - -
120C GLN* 3.4 5.5 + - - +
121C SER* 2.7 45.0 + - - +
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Residues in contact with TYR 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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123B GLN* 3.6 26.2 + - + -
124B HIS* 5.3 7.6 - + - -
7C SER* 4.2 0.9 + - - -
82C ILE* 5.0 2.4 - - - +
86C LYS* 4.1 16.9 + - - -
114C VAL* 3.3 23.5 + - + +
115C GLN 3.7 9.4 - - - +
116C GLN 3.1 1.4 + - - -
117C ARG* 1.3 97.0 - - + +
119C THR* 1.3 59.7 + - - +
120C GLN 3.6 0.2 - - - -
121C SER* 4.8 1.3 - - - +
124C VAL* 3.9 39.3 - - + +
125C ARG 3.6 14.2 - - - +
126C PRO* 3.5 21.5 - - + +
127C PHE* 3.4 38.3 - + + -
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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
------------------------------------------------------------
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