Contacts of the helix formed by residues 155 - 164 (chain A) in PDB entry 3VS5
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 SER 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLY 3.8 2.4 + - - -
154A ILE* 1.3 78.2 - - - +
156A ARG* 1.3 64.0 + - - +
157A LYS* 3.4 8.9 + - - +
158A ASP* 3.0 43.5 + - - -
159A ALA 3.1 10.0 + - - -
176A ARG* 4.1 0.4 - - - -
179A GLU* 3.2 31.4 - - - -
372A GLU* 5.7 0.9 + - - -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 1.3 73.6 - - - +
157A LYS* 1.3 67.7 + - - +
159A ALA* 3.5 1.2 + - - +
160A GLU* 3.1 21.3 + - - +
176A ARG* 3.5 23.1 - - - +
179A GLU* 3.4 18.4 + - - +
180A THR* 6.2 0.4 - - - +
202A HIS* 3.4 36.6 + - + +
517A ASP* 5.9 1.4 - - - +
518A ASP* 3.1 40.4 + - - -
521A THR* 5.4 2.4 - - - +
526A GLN* 3.7 33.6 + - - +
527A PTR 3.3 40.1 + - - +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 3.1 7.9 + - - +
156A ARG* 1.3 86.6 - - - +
158A ASP* 1.3 63.6 + - - +
160A GLU* 2.7 44.0 + - - +
161A ARG* 3.1 38.0 + - - +
179A GLU* 4.9 0.8 + - - -
365A ASP* 4.3 19.3 + - - +
368A ALA* 5.3 1.3 - - - -
372A GLU* 5.9 1.3 - - - +
516A LEU 5.2 1.5 + - - -
517A ASP* 2.8 62.7 + - + +
518A ASP* 5.1 3.6 - - - +
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLY 4.5 4.0 - - - +
154A ILE* 4.0 17.9 - - + +
155A SER* 3.0 39.3 + - - +
157A LYS* 1.3 72.8 - - - +
159A ALA* 1.3 60.4 + - - +
161A ARG* 3.1 22.9 + - - +
162A GLN* 2.8 38.7 + - + +
320A ASP* 5.4 0.8 - - - +
321A LYS* 4.2 14.2 + - - -
372A GLU* 4.8 8.6 - - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.4 15.1 - - + +
155A SER 3.1 4.0 + - - -
156A ARG 3.6 6.7 - - - +
157A LYS 3.4 0.2 - - - -
158A ASP* 1.3 77.3 - - - +
160A GLU* 1.3 62.6 + - - +
162A GLN* 4.1 0.4 - - - +
163A LEU* 3.0 32.5 + - - +
174A MET* 3.7 17.3 - - - -
176A ARG* 3.4 30.5 - - - +
188A SER* 3.7 11.2 - - - +
200A VAL* 4.8 0.2 - - - -
202A HIS* 4.5 0.2 - - + -
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.1 13.7 + - - +
157A LYS* 2.7 47.5 + - - +
159A ALA* 1.3 80.0 - - - +
161A ARG* 1.3 64.5 + - - +
164A LEU* 3.2 47.8 + - + +
200A VAL* 3.8 33.3 - - + +
202A HIS* 4.3 7.4 + - - +
365A ASP* 5.5 1.2 - - - +
517A ASP 4.6 0.2 - - - +
518A ASP* 5.6 1.2 - - - +
521A THR* 5.3 4.5 + - - -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LYS* 3.1 35.9 + - - +
158A ASP* 3.1 27.4 + - - +
160A GLU* 1.3 79.1 - - - +
162A GLN* 1.3 63.7 + - + +
164A LEU* 3.5 5.5 + - - +
165A ALA* 3.4 19.9 + - - +
321A LYS* 4.3 7.9 - - - +
365A ASP* 2.6 42.0 + - - +
368A ALA* 3.5 10.7 - - - +
369A GLN* 3.3 46.3 - - - +
372A GLU* 3.9 14.1 + - - -
399A VAL* 6.5 0.7 - - - -
517A ASP* 3.8 7.3 + - - -
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Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 4.2 17.6 - - - -
154A ILE* 4.9 15.7 - - + +
158A ASP* 2.8 26.2 + - + +
159A ALA 4.1 2.7 - - - +
161A ARG* 1.3 75.6 - - + +
163A LEU* 1.3 56.9 + - - +
165A ALA* 3.4 13.5 - - - +
168A ASN* 3.1 18.7 + - - -
174A MET* 4.1 13.5 - - + -
246A CYS* 3.5 7.0 - - - -
247A MET* 3.6 19.9 - - - +
248A SER* 4.7 3.8 - - - -
249A SER 5.6 0.2 + - - -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ALA 3.0 20.8 + - - +
162A GLN* 1.3 75.4 - - - +
164A LEU* 1.3 53.1 + - - +
165A ALA 3.3 2.9 - - - -
168A ASN* 3.7 6.0 - - - +
172A SER* 3.4 40.6 - - - +
173A PHE* 3.9 0.9 - - - +
174A MET* 4.0 9.4 - - + -
188A SER* 3.4 41.3 - - - +
189A VAL 4.3 0.2 - - - +
190A ARG* 2.7 39.0 + - + +
200A VAL* 3.6 19.5 - - + -
246A CYS* 3.6 28.3 - - + -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 3.2 43.3 + - + +
161A ARG* 3.5 6.9 + - - +
162A GLN 3.4 0.4 - - - -
163A LEU* 1.3 79.7 - - - +
165A ALA* 1.3 61.5 + - - +
166A PRO* 3.9 3.8 - - - +
190A ARG* 3.9 17.7 + - - +
198A ASP* 3.7 42.0 - - + +
199A THR* 4.4 7.9 - - - +
200A VAL* 4.2 8.1 - - + +
362A LYS* 5.7 3.0 + - - -
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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