Contacts of the strand formed by residues 210 - 222 (chain A) in PDB entry 1VAV
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 GLY 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.8 10.7 - - - -
45A VAL 3.1 13.7 - - - -
47A VAL 3.6 4.7 - - - -
91A ALA* 3.8 6.1 - - - +
92A VAL* 3.2 24.5 + - - +
93A PRO* 3.8 15.0 - - - -
208A SER 4.1 0.4 + - - -
209A GLU* 1.3 82.2 - - - +
211A GLY* 1.3 59.9 + - - -
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Residues in contact with GLY 211 (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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44A TRP* 3.2 5.9 - - - -
45A VAL* 2.8 40.9 + - - +
91A ALA 3.3 8.3 - - - -
93A PRO* 4.0 3.0 - - - +
98A MET* 3.7 19.3 - - - -
198A LEU* 3.5 7.3 - - - +
200A LEU* 4.2 0.9 - - - -
210A GLY* 1.3 74.1 - - - -
212A ARG* 1.3 62.4 + - - -
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Residues in contact with ARG 212 (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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42A ARG* 4.3 17.0 - - + +
43A PHE 3.3 13.7 - - - +
44A TRP* 3.9 21.6 - - + -
89A ILE* 3.7 2.1 - - - +
90A GLU* 2.6 84.6 + - + +
91A ALA* 2.9 31.1 + - + +
98A MET* 4.1 0.5 - - - +
198A LEU* 3.5 3.6 - - - +
211A GLY* 1.3 75.5 - - - +
213A ALA* 1.3 66.4 + - - +
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Residues in contact with ALA 213 (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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41A ILE 3.7 0.7 - - - +
42A ARG* 3.5 1.1 - - - -
43A PHE* 2.7 42.9 + - - +
87A LEU* 4.6 8.3 - - + -
88A ARG 3.4 16.8 - - - +
89A ILE* 4.0 11.9 - - + -
90A GLU* 4.2 4.7 - - - +
198A LEU* 3.6 25.4 - - + +
212A ARG* 1.3 78.2 - - - +
214A THR* 1.3 60.6 + - - +
215A PHE* 4.2 4.5 - - + -
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Residues in contact with THR 214 (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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37A THR* 4.3 3.8 - - - +
39A ASP* 3.7 31.0 - - + +
41A ILE 3.1 13.5 - - - +
42A ARG* 3.4 24.3 + - - +
87A LEU* 3.2 2.6 - - - -
88A ARG* 3.1 51.2 + - - +
90A GLU* 2.7 26.2 + - - -
213A ALA* 1.3 73.7 - - - +
215A PHE* 1.3 64.8 + - - +
216A SER* 3.8 2.1 + - - +
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Residues in contact with PHE 215 (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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2A PRO* 4.5 3.6 - - - +
39A ASP 4.1 1.3 - - - -
40A GLY* 3.4 1.6 - - - -
41A ILE* 2.8 36.5 + - + +
43A PHE* 3.4 36.1 - + + -
85A ALA* 3.8 24.0 - - + -
86A THR 3.2 5.6 - - - +
87A LEU* 3.7 29.2 - - + -
100A ILE 3.6 19.1 - - - -
160A TYR* 3.8 22.4 - + - -
196A ALA* 4.5 7.4 - - + -
197A GLY 3.9 17.3 - - - -
198A LEU* 5.2 0.4 - - + -
213A ALA* 4.7 6.7 - - + -
214A THR* 1.3 75.0 - - - +
216A SER* 1.3 62.8 + - - +
217A GLU 3.6 10.0 + - - +
218A LEU* 4.4 14.6 - - + -
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Residues in contact with SER 216 (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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2A PRO* 4.5 10.0 - - - +
39A ASP* 3.2 21.5 - - - -
40A GLY* 4.4 1.4 - - - -
86A THR* 2.8 22.7 + - - +
87A LEU* 4.8 0.7 - - - -
157A PRO* 5.7 0.9 - - - +
214A THR* 3.8 4.1 + - - -
215A PHE* 1.3 72.1 - - - +
217A GLU* 1.3 60.6 + - - +
15B ARG* 2.6 32.3 + - - +
16B PRO* 4.5 5.2 - - - +
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Residues in contact with GLU 217 (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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2A PRO* 4.3 4.3 - - - -
84A GLU* 4.3 6.6 - - - +
85A ALA* 3.2 18.8 + - - +
86A THR* 2.7 54.9 + - - +
159A SER* 5.3 0.5 - - - -
215A PHE* 3.2 4.4 - - - -
216A SER* 1.3 81.6 - - - +
218A LEU* 1.3 68.7 + - - +
219A ARG* 2.6 35.6 + - + -
13B GLN* 6.0 0.5 - - - +
14B GLY* 4.5 4.9 + - - -
15B ARG* 2.7 44.4 + - + +
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Residues in contact with LEU 218 (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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2A PRO* 3.7 31.0 - - + +
3A ASP* 4.5 9.0 + - - +
7A TRP* 3.2 36.4 + - + +
41A ILE* 4.6 11.4 - - + -
43A PHE* 5.2 1.3 - - + -
62A LEU* 3.4 32.5 - - + -
83A LEU* 3.7 16.4 - - + -
84A GLU 3.3 4.9 - - - +
85A ALA* 4.8 1.1 - - + -
196A ALA* 4.3 11.4 - - + -
215A PHE* 4.4 20.6 - - + -
217A GLU* 1.3 78.8 - - - +
219A ARG* 1.3 67.1 + - - +
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Residues in contact with ARG 219 (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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82A TRP 3.9 0.5 - - - +
83A LEU* 3.5 4.6 - - - +
84A GLU* 2.6 73.0 + - - +
217A GLU* 2.6 38.8 + - + -
218A LEU* 1.3 78.6 - - - +
220A VAL* 1.3 63.8 + - - +
221A SER* 6.3 0.7 - - - -
15B ARG* 2.9 39.8 - - - +
48B ASN* 6.0 2.6 - - - +
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Residues in contact with VAL 220 (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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6A THR* 4.7 13.9 + - - +
7A TRP* 3.2 42.1 - - + +
64A GLU* 3.6 27.1 - - + +
82A TRP 3.3 3.6 - - - +
83A LEU* 3.9 12.1 - - + -
194A PHE* 3.9 13.7 - - + -
219A ARG* 1.3 80.5 - - - +
221A SER* 1.3 67.8 + - - +
222A HIS* 4.0 9.0 - - + +
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Residues in contact with SER 221 (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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80A ASP 3.4 2.1 + - - +
81A ASN* 3.4 1.6 - - - -
82A TRP* 2.9 54.0 + - - +
84A GLU* 4.8 4.7 + - - -
219A ARG* 6.3 0.7 - - - -
220A VAL* 1.3 77.7 - - - +
222A HIS* 1.3 69.1 + - - +
223A GLN* 3.9 22.4 - - - +
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Residues in contact with HIS 222 (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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64A GLU* 2.7 24.8 + - - -
72A TYR* 3.5 26.1 - + - +
74A TRP* 3.3 38.0 - + - +
79A ALA* 4.0 10.6 - - + +
80A ASP 3.3 6.3 - - - -
81A ASN* 2.6 32.8 + - + +
194A PHE* 4.0 7.4 - + - -
220A VAL* 4.0 8.4 - - + +
221A SER* 1.3 75.4 + - - +
223A GLN* 1.3 66.6 + - - +
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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