Contacts of the strand formed by residues 3 - 12 (chain B) in PDB entry 1SIW
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 ILE 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 3.0 35.4 - - + -
2B LYS* 1.3 71.5 - - - +
4B ARG* 1.3 74.1 + - - +
274B LEU* 4.3 17.5 - - + -
275B TYR 3.5 4.7 - - - +
301B LEU* 3.4 18.8 - - + -
308B VAL* 4.9 5.2 - - + +
311B GLN* 3.1 30.5 - - + -
312B ALA* 4.1 20.9 - - + +
315B ASP* 2.8 22.4 + - - +
317B ILE* 3.2 30.2 - - + +
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Residues in contact with ARG 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.4 48.1 - - - -
24A LEU* 4.2 24.2 - - - +
2B LYS* 4.2 20.0 - - - +
3B ILE* 1.3 83.3 - - - +
5B SER* 1.3 61.4 + - - +
205B GLU* 4.1 34.2 + - + +
274B LEU* 3.4 4.0 - - - -
275B TYR* 2.9 62.4 + - + +
277B ALA* 3.6 22.4 - - - +
317B ILE* 4.4 4.5 - - - -
221C VAL* 3.7 19.1 - - - +
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Residues in contact with SER 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 1.3 76.6 - - - +
6B GLN* 1.3 64.9 + - - +
205B GLU 4.1 4.5 + - - +
206B GLU 3.2 19.2 + - - +
207B ASP* 3.4 17.9 + - - -
208B GLY 3.5 2.6 + - - -
272B VAL* 4.2 2.9 - - - -
273B LEU 3.6 4.7 - - - -
274B LEU* 3.5 21.5 - - - -
275B TYR* 4.1 4.9 + - - -
317B ILE* 4.3 10.9 - - - +
318B PRO* 5.5 1.2 - - - +
321B VAL* 3.7 24.9 - - - +
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Residues in contact with GLN 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B SER* 1.3 79.9 - - - +
7B VAL* 1.3 79.1 + - - +
8B GLY 3.4 1.0 + - - -
186B HIS* 2.9 33.7 + - - +
188B LEU* 3.5 12.3 - - - +
203B LYS* 2.9 24.4 + - - -
207B ASP* 3.4 16.2 - - - +
208B GLY* 3.3 16.6 + - - -
209B ILE* 5.2 1.4 - - + +
246B PHE* 6.4 0.2 - - - -
272B VAL* 3.4 3.3 - - - -
273B LEU* 2.8 31.4 + - - +
275B TYR* 4.2 7.0 - - + -
352B MET* 3.6 25.8 - - + +
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 1.3 85.8 + - - +
8B GLY* 1.3 69.6 + - - +
207B ASP* 3.8 11.4 + - + +
209B ILE* 6.5 0.2 - - + -
246B PHE* 3.7 32.8 - - + -
251B ILE* 4.5 12.8 - - + -
270B LEU* 4.1 13.9 - - + -
271B GLY* 3.6 18.2 - - - +
272B VAL* 4.2 16.2 - - + +
458B VAL* 4.2 28.0 - - + -
459B PRO* 4.3 5.6 - - + +
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Residues in contact with GLY 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 3.4 8.0 + - - -
7B VAL* 1.3 76.3 - - - +
9B MET* 1.3 59.7 + - - +
246B PHE* 4.8 0.7 - - - -
270B LEU* 3.5 8.8 - - - +
271B GLY 2.7 34.2 + - - -
273B LEU* 4.7 8.2 - - - +
330B VAL* 4.0 12.1 - - - -
352B MET* 3.6 14.4 - - - -
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Residues in contact with MET 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY* 1.3 76.1 - - - +
10B VAL* 1.3 64.6 + - - +
11B LEU* 3.9 23.3 - - + -
183B LEU* 4.0 25.8 - - + -
246B PHE* 3.9 18.6 - - + -
257B THR* 3.9 9.4 - - - +
259B CYS* 4.3 5.2 - - - -
260B SER* 3.2 25.6 - - - +
268B ARG* 4.2 15.0 - - + -
269B TYR 3.2 11.4 - - - +
270B LEU* 3.6 12.8 - - + -
330B VAL* 4.2 2.3 - - - +
352B MET 3.3 6.8 + - - +
353B VAL* 3.2 14.7 - - + +
354B TRP* 2.7 31.9 + - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 1.3 80.0 - - - +
11B LEU* 1.3 65.8 + - - +
12B ASN 4.7 0.4 - - - +
267B ILE 3.5 1.7 - - - +
268B ARG* 3.5 3.3 - - - -
269B TYR* 2.9 38.6 + - + -
330B VAL* 3.9 32.1 - - + +
333B MET* 3.8 26.9 - - + -
334B ALA* 5.3 1.1 - - + -
340B ALA* 3.8 30.7 - - + -
354B TRP* 3.2 12.1 - - + +
356B VAL* 4.0 13.7 - - + -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.9 11.9 - - - -
10B VAL* 1.3 79.0 - - - +
12B ASN* 1.3 59.8 + - - +
13B LEU* 3.2 5.2 + - + -
181B PRO* 3.5 32.5 - - + +
183B LEU* 4.7 2.5 - - + -
267B ILE* 3.6 12.6 - - + -
268B ARG* 3.5 42.2 - - + +
353B VAL* 3.5 32.8 - - + -
354B TRP 2.9 12.0 + - - +
355B TYR* 3.3 23.1 - - + +
356B VAL 3.0 22.3 + - - -
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Residues in contact with ASN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A TYR* 3.0 22.9 + - - -
10B VAL* 4.2 1.0 - - + +
11B LEU* 1.3 69.5 - - - +
13B LEU* 1.3 63.4 + - - +
14B ASP* 3.0 21.3 + - - +
15B LYS* 3.1 27.0 + - + +
16B CYS 3.4 7.4 + - - -
267B ILE* 3.0 34.4 + - + +
269B TYR* 4.7 7.8 - - + -
333B MET* 6.2 0.4 - - - -
356B VAL* 3.6 26.4 - - + +
409B MET* 5.4 1.0 - - - -
447B LEU* 3.8 22.1 - - + +
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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