Contacts of the helix formed by residues 131 - 148 (chain C) in PDB entry 6VSU
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 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C GLY 3.5 3.9 + - - +
130C VAL* 1.3 77.3 - - - +
132C ASP* 1.3 63.8 + - - +
133C ASP* 2.9 30.7 + - - +
134C ARG* 3.1 18.5 + - - +
135C LEU* 3.1 17.7 + - - +
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Residues in contact with ASP 132 (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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74C HIS* 3.1 35.0 + - - -
75C ASN* 3.4 22.9 + - - +
126C ARG* 5.9 0.3 - - - +
130C VAL 5.6 0.2 - - - +
131C ASP* 1.3 72.3 - - - +
133C ASP* 1.3 57.8 + - - +
135C LEU* 3.1 7.9 + - - +
136C MET* 2.8 49.9 + - - +
197C ASN* 6.1 0.2 - - - -
199C TYR* 3.7 21.4 - - + +
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Residues in contact with ASP 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASP* 2.9 13.9 + - - +
132C ASP* 1.3 77.9 - - - +
134C ARG* 1.3 60.0 + - + +
136C MET* 3.4 1.7 + - - +
137C ASN* 2.4 37.7 + - - +
198C LYS* 3.4 16.6 + - - -
199C TYR* 2.9 29.1 + - - -
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Residues in contact with ARG 134 (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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30C GLU* 4.0 16.2 + - - -
33C GLN* 3.0 43.8 + - - +
34C ASN* 2.8 26.8 + - - +
37C ILE* 3.8 18.7 - - + +
130C VAL* 3.6 21.9 - - + +
131C ASP* 3.1 21.5 + - - +
133C ASP* 1.3 72.5 - - + +
135C LEU* 1.3 53.8 + - - +
137C ASN* 3.2 9.3 + - - +
138C VAL* 2.8 40.9 + - - +
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Residues in contact with LEU 135 (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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72C LEU* 3.9 9.4 - - + -
74C HIS* 3.7 32.3 - - + +
120C VAL* 5.6 0.4 - - + -
122C VAL* 3.9 15.7 - - + -
125C ILE* 4.1 30.1 - - + -
126C ARG* 3.8 19.3 - - + +
130C VAL* 3.8 9.7 - - + +
131C ASP 3.1 12.8 + - - +
132C ASP* 3.1 14.0 + - - +
134C ARG* 1.3 75.0 - - - +
136C MET* 1.3 59.0 + - - +
138C VAL* 3.0 9.7 + - + +
139C ILE* 2.8 48.0 + - + +
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Residues in contact with MET 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 3.9 21.8 - - + -
75C ASN* 4.1 5.2 - - - +
132C ASP* 2.8 42.3 + - - +
133C ASP 4.0 3.4 - - - +
135C LEU* 1.3 72.8 - - - +
137C ASN* 1.3 52.4 + - - +
139C ILE* 3.2 21.6 + - + +
140C SER* 2.8 34.1 + - - -
162C SER* 4.2 13.0 - - - +
163C ILE* 4.4 3.8 - - - -
165C TYR* 5.9 0.2 - - + -
166C PRO* 3.2 43.8 - - + +
169C ARG* 3.7 8.5 - - - +
199C TYR* 3.6 34.8 - - + +
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Residues in contact with ASN 137 (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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133C ASP* 2.4 42.6 + - - +
134C ARG* 3.5 10.7 - - - +
136C MET* 1.3 73.9 - - - +
138C VAL* 1.3 53.5 - - - +
140C SER* 3.0 4.7 + - - -
141C GLU* 2.7 47.4 + - + +
169C ARG* 3.3 28.2 + - - +
199C TYR* 5.1 2.0 + - - -
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Residues in contact with VAL 138 (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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37C ILE* 3.7 40.8 - - + -
40C SER* 5.2 2.9 - - - -
41C LEU* 3.7 18.7 - - + +
120C VAL* 4.5 8.3 - - + -
125C ILE* 3.6 26.5 - - + -
134C ARG 2.8 23.8 + - - +
135C LEU* 3.3 11.4 - - + +
137C ASN* 1.3 70.1 - - - +
139C ILE* 1.3 53.7 + - - +
141C GLU* 3.2 9.0 + - - +
142C SER* 2.5 40.9 + - - +
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Residues in contact with ILE 139 (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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70C VAL* 3.6 35.7 - - + -
72C LEU* 3.6 32.1 - - + -
120C VAL* 4.7 11.9 - - + -
122C VAL* 4.7 1.1 - - + -
135C LEU* 2.8 30.7 + - + +
136C MET* 3.3 24.0 - - + +
138C VAL* 1.3 72.8 - - - +
140C SER* 1.3 62.6 + - - +
142C SER* 3.2 10.2 + - - -
143C VAL* 3.1 23.3 + - + +
163C ILE* 4.7 1.8 - - + +
166C PRO* 4.2 15.5 - - + -
167C VAL* 4.6 13.0 - - + -
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Residues in contact with SER 140 (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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136C MET 2.8 13.2 + - - -
137C ASN* 3.4 8.1 - - - -
139C ILE* 1.3 71.8 - - - +
141C GLU* 1.3 66.7 + - - +
143C VAL* 3.2 3.0 + - - -
144C LYS* 3.0 32.3 + - - +
166C PRO* 2.9 23.5 + - - +
169C ARG* 3.0 34.0 + - - -
170C ALA* 3.2 18.7 - - - +
173C GLU* 5.5 0.9 - - - -
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Residues in contact with GLU 141 (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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41C LEU* 3.8 21.5 - - + -
137C ASN* 2.7 31.6 + - + +
138C VAL* 3.5 7.0 - - - +
140C SER* 1.3 74.5 - - - +
142C SER* 1.3 57.5 + - - +
144C LYS* 3.1 29.5 + - - +
145C LEU* 2.9 34.6 + - + +
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Residues in contact with SER 142 (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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41C LEU* 3.6 10.5 - - - +
44C ILE* 4.0 14.1 - - - +
68C LEU* 4.2 5.2 - - - -
120C VAL* 3.7 34.6 - - - +
138C VAL* 2.5 24.0 + - - +
139C ILE 3.2 6.9 + - - -
141C GLU* 1.3 76.1 - - - +
143C VAL* 1.3 61.4 + - - +
145C LEU* 3.2 27.5 + - - +
146C VAL* 3.4 13.0 + - - +
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Residues in contact with VAL 143 (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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68C LEU* 3.8 22.2 - - + -
139C ILE* 3.1 17.5 + - + +
140C SER* 3.2 7.2 + - - +
142C SER* 1.3 73.7 - - - +
144C LYS* 1.3 63.2 + - - +
146C VAL* 3.2 16.0 + - - +
147C MET* 3.3 28.0 + - - +
154C PRO* 4.1 17.7 - - + -
156C VAL* 4.4 1.1 - - + -
167C VAL* 4.0 44.0 - - + +
170C ALA* 4.0 14.1 - - + -
171C VAL* 4.1 0.7 - - + -
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Residues in contact with LYS 144 (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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140C SER* 3.0 22.1 + - - +
141C GLU* 3.1 31.6 + - - +
143C VAL* 1.3 75.5 - - - +
145C LEU* 1.3 59.0 + - + +
147C MET* 3.2 11.1 + - - +
148C GLU* 2.9 43.3 + - - +
170C ALA* 3.7 32.5 - - + +
173C GLU* 2.8 38.3 + - - +
174C LYS* 4.4 11.4 - - + +
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Residues in contact with LEU 145 (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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41C LEU* 3.5 46.7 - - + +
44C ILE* 4.2 16.6 - - + -
45C ARG* 4.1 32.3 - - + +
48C ALA* 4.1 3.5 - - + +
141C GLU* 2.9 21.2 + - + +
142C SER* 3.2 10.3 + - - +
144C LYS* 1.3 79.4 - - + +
146C VAL* 1.3 60.4 + - - +
148C GLU* 3.7 13.1 + - + +
149C GLU* 3.2 23.9 + - - +
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Residues in contact with VAL 146 (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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44C ILE* 4.8 4.3 - - + -
48C ALA* 4.7 4.3 - - + -
66C SER* 3.9 29.4 - - - +
68C LEU* 4.3 15.7 - - + -
117C VAL* 3.9 26.0 - - + -
142C SER 3.5 15.3 - - - +
143C VAL 3.2 6.8 + - - +
145C LEU* 1.3 76.6 - - - +
147C MET* 1.3 58.0 + - - +
149C GLU* 3.0 32.8 + - - +
152C LEU* 3.8 15.0 - - + +
153C ARG 4.8 0.2 - - - -
154C PRO* 4.5 20.0 - - + -
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Residues in contact with MET 147 (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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143C VAL* 3.5 23.3 - - - +
144C LYS* 3.2 9.1 + - - +
146C VAL* 1.3 76.8 - - - +
148C GLU* 1.3 60.0 + - - +
149C GLU 3.1 7.7 + - - +
150C GLU* 4.2 11.8 - - - +
152C LEU 4.1 12.3 - - - +
154C PRO* 4.0 20.4 - - + -
170C ALA 3.9 3.4 - - - +
171C VAL* 3.7 33.0 - - + -
174C LYS* 3.3 51.6 + - + -
175C LEU* 3.6 25.6 - - + -
307C VAL* 5.4 2.5 - - + +
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Residues in contact with GLU 148 (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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144C LYS* 2.9 29.8 + - - +
145C LEU* 3.9 12.6 - - + +
146C VAL 3.2 0.2 - - - -
147C MET* 1.3 73.5 - - - +
149C GLU* 1.3 66.2 + - + +
150C GLU* 3.7 9.7 + - - +
174C LYS* 3.7 32.2 - - - +
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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