Contacts of the strand formed by residues 303 - 315 (chain F) in PDB entry 1SID
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 PRO 303 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F PHE* 5.3 3.8 - - + -
53F LEU 3.5 5.2 - - - +
54F ASN* 3.3 29.4 - - - +
55F PRO* 3.2 12.8 - - + -
129F VAL* 3.4 7.1 - - - +
130F VAL* 3.2 48.3 + - + +
284F ASP* 4.6 0.4 - - - -
300F ARG* 5.8 1.1 - - - +
302F LEU* 1.3 97.9 - - + +
304F ARG* 1.3 62.7 + - - +
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Residues in contact with ARG 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F PHE* 2.8 34.7 - - - -
53F LEU 2.8 19.1 + - - +
127F THR* 3.0 37.6 + - - +
128F GLU 3.4 8.1 - - - +
129F VAL* 3.5 18.9 - - + +
130F VAL* 5.4 1.6 - - - -
163F HIS* 4.3 9.7 - - - +
164F VAL 3.9 5.7 + - - +
165F PHE* 4.1 21.4 - - - -
282F CYS* 3.7 19.0 - - - +
284F ASP* 2.6 53.7 + - - +
303F PRO* 1.3 76.9 - - - +
305F TYR* 1.3 57.6 + - - +
306F PHE* 3.2 29.1 - - + -
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Residues in contact with TYR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLU* 2.6 40.4 + - + +
51F ALA 3.4 12.8 - - - -
52F PHE* 3.9 4.5 - - + -
126F LYS* 4.0 13.6 - - + +
127F THR* 2.4 41.8 + - - -
128F GLU* 2.8 25.2 + - + +
130F VAL* 5.1 7.3 - - + +
304F ARG* 1.3 71.3 - - - +
306F PHE* 1.3 66.9 + - - +
307F LYS* 3.5 34.4 - - + +
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Residues in contact with PHE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLU* 2.8 28.6 - - - +
51F ALA 2.8 14.9 + - - +
52F PHE* 4.2 5.8 - - - -
53F LEU* 3.9 27.1 - - + -
125F VAL* 4.7 4.3 - - + -
126F LYS 3.5 4.9 - - - -
127F THR* 4.3 3.1 - - - -
165F PHE* 4.2 18.8 - + + -
166F ALA 4.4 5.2 - - - -
167F VAL* 4.5 8.7 - - + -
280F LEU* 3.5 40.2 - - + -
281F SER 4.4 1.1 - - - -
282F CYS* 4.1 8.1 - - + -
304F ARG* 3.2 46.9 - - + -
305F TYR* 1.3 95.8 - - - +
307F LYS* 1.3 61.1 - - - +
308F ILE* 3.6 13.5 - - + -
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Residues in contact with LYS 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F GLU* 3.3 40.2 + - + -
49F ILE 3.3 5.2 - - - +
50F GLU* 3.7 18.7 + - + +
125F VAL* 3.1 6.1 - - - +
126F LYS* 2.7 61.7 + - + +
305F TYR* 3.5 27.6 - - + +
306F PHE* 1.3 75.6 - - - +
308F ILE* 1.3 64.0 + - - +
309F THR* 3.6 8.0 + - - +
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Residues in contact with ILE 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F THR 3.4 2.4 - - - +
48F GLU* 3.4 5.2 - - - -
49F ILE* 2.8 41.3 + - + +
50F GLU* 5.5 0.2 - - - -
51F ALA* 5.7 0.4 - - + +
103F LEU* 6.4 0.4 - - + -
122F ALA* 4.3 12.8 - - + -
124F SER 3.5 7.9 - - - +
125F VAL* 4.1 12.1 - - + -
167F VAL* 4.7 3.4 - - + -
263F LEU* 4.3 1.6 - - + -
278F LEU* 4.0 20.6 - - + -
280F LEU* 4.0 22.0 - - + -
306F PHE* 3.6 26.0 - - + -
307F LYS* 1.3 75.9 - - - +
309F THR* 1.3 70.9 + - - +
310F LEU* 3.4 30.6 + - + +
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Residues in contact with THR 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 4.7 11.2 - - + -
47F THR 3.5 4.0 - - - +
48F GLU* 4.2 24.1 - - + +
123F VAL* 2.8 31.8 + - + +
124F SER* 2.7 33.3 + - - +
125F VAL 4.2 0.3 + - - -
260F THR* 4.5 6.3 - - + +
307F LYS* 3.6 12.7 + - - +
308F ILE* 1.3 75.8 - - - +
310F LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 3.1 20.9 - - - +
47F THR* 3.1 43.9 + - - +
49F ILE* 4.7 10.3 - - + -
105F LEU* 4.4 19.1 - - + -
120F TRP* 4.5 7.4 - - + -
121F GLU 2.8 26.5 - - - +
122F ALA* 3.7 5.6 - - - +
123F VAL* 4.1 2.2 - - - -
273F CYS* 4.9 3.4 - - - -
278F LEU* 3.2 38.6 - - + -
308F ILE* 3.4 13.9 - - + +
309F THR* 1.3 76.5 - - - +
311F ARG* 1.3 58.7 + - - +
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Residues in contact with ARG 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ASP* 5.9 2.0 - - - +
45F SER 4.3 10.8 - - - +
46F VAL* 4.7 7.0 - - + -
119F MET 3.5 0.7 - - - +
120F TRP* 3.5 7.5 - - - -
121F GLU* 2.7 78.7 + - + +
123F VAL* 3.9 13.1 - - + +
264F LEU* 4.1 11.9 - - - +
268F GLY 3.5 7.9 + - - -
310F LEU* 1.3 74.0 - - - +
312F LYS* 1.3 72.0 + - - +
313F ARG* 2.9 34.0 - - - +
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Residues in contact with LYS 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F VAL 5.0 0.8 + - - -
41F THR* 2.8 29.8 + - - -
42F GLY 2.3 36.8 + - - +
43F PRO* 3.3 25.3 + - + +
45F SER* 3.3 18.4 + - - +
108F LEU* 3.8 33.4 - - + +
109F ASN* 4.4 6.1 + - - -
118F GLN* 4.1 23.2 - - - +
119F MET 3.5 5.4 - - - -
120F TRP* 3.8 14.1 - - + -
311F ARG* 1.3 81.2 - - - +
313F ARG* 1.3 62.2 + - - +
314F TRP* 4.3 2.8 + - - -
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Residues in contact with ARG 313 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C VAL* 4.3 16.9 - - - +
118F GLN* 4.0 1.8 - - - -
119F MET* 2.6 42.7 + - - +
121F GLU* 2.7 39.0 + - + +
268F GLY 2.5 30.9 + - - -
269F VAL* 3.1 22.9 - - - +
272F LEU* 4.6 6.3 - - + +
311F ARG* 2.9 19.1 + - - +
312F LYS* 1.3 76.3 - - - +
314F TRP* 1.3 81.6 + - + +
315F VAL* 3.5 13.2 - - + +
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Residues in contact with TRP 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C VAL* 4.1 6.1 - - - +
43F PRO* 6.0 3.0 - - - +
109F ASN* 3.8 19.3 - - + -
110F GLU 4.6 0.9 - - - -
111F ASP* 4.4 10.3 - - + -
116F THR* 3.0 45.3 - - + +
117F LEU* 3.1 8.3 - - - -
118F GLN* 3.1 60.5 + - + -
312F LYS 5.6 2.0 - - - -
313F ARG* 1.3 90.4 - - + +
315F VAL* 1.3 59.7 + - - +
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Residues in contact with VAL 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C PRO* 6.3 0.2 - - - -
360C VAL* 3.2 17.0 - - + +
361C PRO 3.7 10.3 - - - +
362C GLY* 3.5 15.7 - - - +
116F THR* 2.8 21.0 + - - -
117F LEU* 2.6 29.7 + - + +
119F MET* 3.7 22.9 - - + -
272F LEU* 4.3 15.0 - - + -
313F ARG* 3.5 17.0 - - - +
314F TRP* 1.3 79.9 - - - +
316F LYS* 1.3 75.3 + - - +
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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