Contacts of the helix formed by residues 108 - 122 (chain C) in PDB entry 6N0M
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 ALA 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PRO 4.3 0.4 + - - -
107C LEU* 1.3 72.7 - - - +
109C SER* 1.3 56.1 + - - +
110C SER* 3.3 12.6 - - - +
111C TRP* 2.8 36.2 + - + +
112C ARG* 3.0 9.5 + - - +
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Residues in contact with SER 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU 3.6 5.0 + - - -
102C HIS* 5.3 0.3 - - - -
107C LEU 3.7 1.2 + - - -
108C ALA* 1.3 72.7 - - - +
110C SER* 1.3 64.4 + - - +
112C ARG* 3.2 31.4 + - - +
113C HIS* 2.9 49.0 + - - -
139C THR* 3.5 20.9 + - - -
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Residues in contact with SER 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA* 4.2 8.7 - - - +
109C SER* 1.3 75.8 - - - +
111C TRP* 1.3 70.1 + - - +
113C HIS* 3.5 0.3 + - - +
114C TYR* 3.0 23.0 + - - +
136C PHE* 3.3 18.0 - - - -
139C THR* 3.5 21.2 + - - +
140C GLY 4.6 2.9 - - - -
141C GLY* 3.8 29.4 - - - -
145C TRP* 5.2 2.2 - - - -
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Residues in contact with TRP 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU* 4.3 21.1 - - + -
108C ALA* 2.8 28.6 + - + +
110C SER* 1.3 81.8 + - - +
112C ARG* 1.3 59.4 + - - +
114C TYR* 3.2 7.4 + - - +
115C ILE* 2.9 37.6 + - + +
145C TRP* 3.4 27.0 - + - -
153C PRO* 4.0 21.1 - - + -
155C LYS* 3.8 48.2 - - + -
156C LEU* 3.1 32.9 - - + +
187C HIS* 6.2 0.2 - - + -
189C TRP* 4.8 2.2 - + - -
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Residues in contact with ARG 112 (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 LEU 2.6 26.0 + - - +
101C LEU* 3.7 11.1 + - + +
102C HIS* 4.2 1.0 - - - +
103C THR 3.1 42.4 + - - +
104C ASP* 4.5 1.6 - - - +
105C GLY* 4.0 10.3 - - - +
107C LEU* 2.6 41.8 + - + +
108C ALA* 3.0 7.1 + - - +
109C SER* 3.2 37.1 + - - +
111C TRP* 1.3 76.1 - - - +
113C HIS* 1.3 58.8 + - + +
115C ILE* 3.3 6.4 + - - +
116C ALA* 3.0 27.3 + - - +
196C GLN* 3.2 28.7 - - - +
200C LEU* 3.9 24.8 - - + +
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Residues in contact with HIS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 3.6 32.4 + - + +
102C HIS* 4.4 2.4 + + - -
109C SER* 2.9 41.7 + - - +
110C SER 3.9 3.6 - - - +
112C ARG* 1.3 74.0 - - + +
114C TYR* 1.3 64.4 + - - +
116C ALA* 3.2 6.5 + - - +
117C ILE* 3.0 27.5 + - - +
132C HIS* 3.2 27.7 + - + +
135C GLU* 3.6 33.4 + - + +
136C PHE* 3.9 21.8 - - - +
139C THR* 4.0 15.8 - - + -
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Residues in contact with TYR 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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110C SER 3.0 17.1 + - - +
111C TRP 3.2 4.9 + - - +
113C HIS* 1.3 75.0 - - - +
115C ILE* 1.3 62.9 + - - +
117C ILE* 3.0 19.0 + - + +
118C MET* 3.0 36.8 + - + +
136C PHE* 4.1 13.4 - + + -
145C TRP* 2.9 53.9 + + + -
146C LEU* 4.4 3.8 - - + -
148C GLY 3.1 15.1 + - - -
149C LEU* 3.6 19.2 - - + -
152C ALA* 3.7 20.4 - - + -
156C LEU* 3.4 25.1 - - + -
315C PHE* 3.3 26.6 - + - -
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Residues in contact with ILE 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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107C LEU* 3.6 30.5 - - + -
111C TRP* 2.9 23.8 + - + +
112C ARG* 3.4 9.2 - - - +
114C TYR* 1.3 75.3 - - - +
116C ALA* 1.3 58.7 + - - +
118C MET* 3.0 11.6 + - - +
119C ALA* 2.8 27.2 + - - +
156C LEU* 4.5 14.8 - - + -
159C LEU* 3.8 24.9 - - + -
189C TRP* 4.4 6.5 - - + -
197C ALA* 4.3 4.9 - - + +
200C LEU* 4.0 22.4 - - + -
201C LEU* 3.7 25.3 - - + +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.4 4.9 - - + -
112C ARG 3.0 13.0 + - - +
113C HIS* 3.4 9.6 - - - +
115C ILE* 1.3 79.2 - - - +
117C ILE* 1.3 55.3 + - - +
119C ALA* 3.7 3.4 + - - +
120C ALA* 2.9 29.3 + - - +
132C HIS* 3.3 34.0 - - + +
200C LEU* 4.7 2.7 - - + +
204C CYS* 3.4 25.2 - - - +
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Residues in contact with ILE 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 HIS 3.0 19.4 + - - +
114C TYR* 3.0 21.3 + - + +
116C ALA* 1.3 73.0 - - - +
118C MET* 1.3 58.0 + - - +
120C ALA* 3.1 5.0 + - - +
121C ALA* 2.7 37.6 + - - +
129C VAL* 3.7 28.3 - - + +
132C HIS* 3.8 15.9 - - + +
133C MET* 3.7 32.5 - - + +
136C PHE* 4.4 2.7 - - + -
146C LEU* 4.1 14.1 - - + -
315C PHE* 3.9 30.1 - - + -
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Residues in contact with MET 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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114C TYR* 3.0 43.7 + - + +
115C ILE* 3.0 15.7 + - - +
117C ILE* 1.3 78.9 - - + +
119C ALA* 1.3 62.7 - - - +
121C ALA* 3.3 10.1 + - - +
122C ARG* 3.4 8.3 + - - +
149C LEU* 3.8 16.6 - - + -
156C LEU* 3.5 30.5 - - - +
159C LEU* 4.4 8.3 - - + -
160C SER* 3.6 32.1 - - - +
163C ASN* 3.3 21.1 + - + +
201C LEU* 5.0 1.8 - - + -
315C PHE* 4.0 19.8 - - + +
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Residues in contact with ALA 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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115C ILE 2.8 14.6 + - - +
116C ALA* 3.7 0.9 - - - +
118C MET* 1.3 77.0 - - - +
120C ALA* 1.3 62.4 + - - +
122C ARG* 3.3 12.8 + - - +
123C HIS* 4.3 1.4 + - - -
163C ASN* 3.5 13.2 - - - +
201C LEU* 3.6 38.3 - - + +
204C CYS* 3.7 17.3 - - + -
205C HIS* 3.2 18.9 - - - +
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Residues in contact with ALA 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 ALA 2.9 20.3 + - - +
117C ILE 3.7 3.1 - - - +
119C ALA* 1.3 72.9 - - - +
121C ALA* 1.3 66.8 + - - +
123C HIS* 3.0 13.9 + - - +
125C CYS* 3.4 19.0 + - + +
128C LEU* 3.6 31.0 - - + -
129C VAL* 3.7 16.2 - - + +
204C CYS* 4.3 3.3 - - + +
208C SER* 3.9 11.7 - - - +
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Residues in contact with ALA 121 (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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117C ILE 2.7 21.4 + - - +
118C MET 3.3 6.9 + - - +
120C ALA* 1.3 72.5 - - - +
122C ARG* 1.3 54.0 + - - +
124C GLN* 2.8 33.1 + - - +
125C CYS 4.8 0.2 - - - +
129C VAL* 3.7 10.5 - - + +
312C MET* 3.9 14.3 - - + +
315C PHE* 3.6 26.0 - - + -
316C VAL* 3.6 16.4 - - + +
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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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118C MET 3.4 0.6 + - - +
119C ALA 3.3 13.5 - - - +
120C ALA 3.1 0.6 + - - -
121C ALA* 1.3 78.1 - - - +
123C HIS* 1.3 60.6 + - + +
124C GLN* 3.8 2.9 + - - +
160C SER 5.3 1.0 + - - -
163C ASN* 3.4 36.3 - - - +
164C LYS* 3.8 21.5 - - - +
167C ALA* 4.0 10.8 - - + -
168C HIS* 3.3 51.2 + - - +
205C HIS* 4.0 3.8 - - - +
316C VAL* 3.7 20.4 - - - +
317C GLU 2.9 28.5 + - - -
318C ASP 3.4 15.3 + - - -
319C PRO 3.7 16.2 + - - +
321C PHE* 3.6 14.6 + - - +
433C GLU* 4.3 1.7 - - - +
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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
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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