Contacts of the strand formed by residues 237 - 248 (chain P) in PDB entry 1VF5
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 VAL 237 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30P LYS* 3.7 18.2 + - - +
54P TYR* 4.4 25.7 + - + +
58P LEU* 5.3 11.2 - - + -
59P GLN 4.1 13.7 - - - +
60P GLN* 3.4 39.7 - - + +
156P GLY* 5.8 0.7 - - - -
169P ASN* 4.6 2.5 + - - +
234P ASN 5.4 1.3 - - - +
235P PRO* 3.4 14.1 - - + +
236P ASN* 1.3 76.3 + - - +
238P GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P HIS* 5.7 0.3 + - - +
28P ALA* 3.0 21.4 - - - +
30P LYS* 4.4 7.2 - - - -
54P TYR* 6.4 0.4 - - - -
155P ARG* 3.5 20.1 - - - +
156P GLY* 4.2 10.7 - - - +
157P ARG 4.8 1.7 - - - +
159P GLN* 4.5 3.8 + - - +
169P ASN* 5.5 0.2 - - - +
236P ASN* 3.2 9.8 + - - +
237P VAL* 1.3 83.0 - - - +
239P GLY* 1.3 59.5 + - - -
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Residues in contact with GLY 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P HIS* 4.9 4.0 - - - -
28P ALA* 2.8 18.8 - - - -
30P LYS* 3.8 8.5 - - - +
154P ASN* 3.6 7.7 - - - -
155P ARG* 2.8 51.4 + - - +
238P GLY* 1.3 75.3 - - - -
240P PHE* 1.3 61.7 + - - -
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Residues in contact with PHE 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P ILE* 3.5 22.7 - - + -
22P CYS* 3.4 29.4 - - + -
23P ALA* 4.0 20.9 - - + -
26P HIS* 3.6 19.3 + - + +
28P ALA 2.7 6.6 + - - +
29P ALA* 3.3 10.0 - - - +
30P LYS 2.9 21.8 + - - -
152P GLY* 3.1 44.2 - - - -
153P ALA 2.7 21.3 - - - -
154P ASN* 3.8 12.2 - - - +
239P GLY* 1.3 73.4 - - - -
241P GLY* 1.3 62.5 + - - +
242P GLN* 3.2 31.4 - - + -
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Residues in contact with GLY 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P LYS 3.1 16.6 - - - -
31P PRO 3.8 1.1 - - - -
32P ALA* 3.1 16.9 - - - +
152P GLY* 3.6 1.4 - - - -
153P ALA 2.8 31.8 + - - -
155P ARG* 4.1 0.6 - - - +
240P PHE* 1.3 79.1 - - - +
242P GLN* 1.3 62.8 + - - -
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Residues in contact with GLN 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLY 3.5 15.8 + - - -
19P ARG* 3.5 10.3 - - - +
20P ILE* 3.0 38.1 + - - +
23P ALA* 5.2 1.6 - - - +
32P ALA* 3.8 10.0 + - - +
150P HIS* 6.3 0.2 - - - +
151P LEU 3.1 12.4 + - - +
240P PHE* 3.2 30.2 - - + -
241P GLY* 1.3 73.6 - - - -
243P ASP* 1.3 65.4 + - - +
244P ASP* 5.1 10.0 + - - +
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Residues in contact with ASP 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA 3.4 20.8 - - - +
33P GLU* 3.8 7.9 - - - -
34P VAL* 3.2 21.9 + - + +
151P LEU* 3.0 32.8 + - + +
242P GLN* 1.3 79.8 - - - +
244P ASP* 1.3 74.3 + - - +
1S MET* 3.0 44.0 + - - +
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Residues in contact with ASP 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ARG* 4.9 1.3 + - - -
148P ALA* 6.4 0.9 - - + -
149P ILE 3.5 8.3 - - - +
150P HIS* 3.2 32.1 - - + +
151P LEU 4.3 1.0 + - - -
242P GLN* 5.1 9.7 + - - +
243P ASP* 1.3 94.7 + - - +
245P THR* 1.3 69.7 + - - +
1S MET* 3.7 12.5 - - - +
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Residues in contact with THR 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P VAL* 3.8 29.1 + - + +
36P VAL* 4.4 11.1 + - + +
148P ALA* 3.4 6.4 - - - +
149P ILE* 2.9 46.4 + - + +
244P ASP* 1.3 81.9 - - - +
246P GLU* 1.3 87.2 + - - +
1S MET* 3.4 21.4 - - + +
4S GLU* 4.5 5.2 + - - -
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Residues in contact with GLU 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O ASP* 5.0 1.8 - - - +
61O MET* 4.6 9.5 - - + +
36P VAL* 4.3 7.5 - - - +
37P PRO 4.6 1.2 - - - +
38P GLN* 4.2 6.8 - - - +
146P LYS* 3.3 41.2 + - + +
147P TYR 3.0 20.4 - - - +
148P ALA* 4.5 1.3 - - + -
149P ILE* 4.7 2.0 - - - +
245P THR* 1.3 95.0 + - - +
247P ILE* 1.3 59.4 + - - +
248P VAL* 5.9 0.2 - - + -
1R MET* 5.9 3.3 - - - +
2R ILE* 5.2 9.7 + - - +
4S GLU* 5.1 7.7 - - - +
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Residues in contact with ILE 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P VAL* 4.0 11.0 - - + -
37P PRO* 3.1 26.2 - - + +
38P GLN 3.2 5.8 - - - +
39P SER* 3.8 5.6 - - - -
40P VAL* 3.5 37.7 - - + -
46P PHE* 4.1 14.6 - - + -
79P PRO* 4.4 9.4 - - + -
82P PHE* 4.4 20.4 - - + -
145P GLY 3.8 1.0 - - - +
146P LYS* 3.6 0.8 - - - -
147P TYR* 3.0 26.2 + - + +
149P ILE* 3.8 17.5 - - + -
246P GLU* 1.3 74.9 - - - +
248P VAL* 1.3 70.1 + - - +
249P LEU 3.9 0.7 + - - +
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Residues in contact with VAL 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O LEU 4.4 0.9 - - - +
58O ASP* 4.3 0.4 - - - +
59O PRO* 3.5 32.8 - - + -
38P GLN* 2.7 27.4 + - - +
39P SER* 3.0 28.3 - - - -
40P VAL 3.0 8.8 + - - -
145P GLY* 3.4 9.4 - - - +
146P LYS* 3.7 24.0 - - + -
246P GLU* 5.9 0.2 - - + -
247P ILE* 1.3 72.6 - - - +
249P LEU* 1.3 65.1 + - - +
250P GLN* 2.9 39.9 + - + +
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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