Contacts of the strand formed by residues 1 - 13 (chain A) in PDB entry 3K57
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 MET 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1A PRO 3.1 8.3 + - - +
0A HIS* 1.3 82.7 - - - +
2A ALA* 1.3 65.8 + - - +
3A GLN* 3.9 22.4 - - + +
126A VAL 3.8 1.0 - - - +
127A GLU* 3.6 3.0 - - - -
128A GLY 3.2 24.6 + - - +
130A MET* 3.4 36.3 - - - -
135A ILE* 4.3 15.0 - - + +
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Residues in contact with ALA 2 (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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0A HIS* 6.2 0.2 - - + -
1A MET* 1.3 82.0 - - - +
3A GLN* 1.3 66.6 + - - +
125A TRP* 4.9 10.2 - - + -
126A VAL 3.3 9.2 - - - +
127A GLU* 4.0 19.5 - - + +
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Residues in contact with GLN 3 (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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1A MET* 3.9 30.0 - - + +
2A ALA* 1.3 78.5 - - - +
4A ALA* 1.3 65.9 + - - +
27A THR* 3.8 21.5 + - - -
28A ASP 5.4 0.3 + - - -
29A ASN* 4.6 13.0 + - - +
32A LEU* 3.7 25.4 - - + +
125A TRP* 3.3 14.6 - - - -
126A VAL* 2.9 48.7 + - + +
130A MET* 5.0 1.4 - - - +
135A ILE* 5.2 1.0 - - + +
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Residues in contact with ALA 4 (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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3A GLN* 1.3 79.8 - - - +
5A GLY* 1.3 59.7 + - - +
27A THR* 3.8 22.1 - - - +
28A ASP 4.8 0.7 + - - -
124A VAL 3.3 5.8 - - - -
125A TRP* 3.4 11.9 - - + -
126A VAL* 5.5 0.4 - - - -
143A HIS* 3.7 26.5 - - + +
146A TYR* 3.7 26.3 - - + -
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Residues in contact with GLY 5 (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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3A GLN 4.0 0.4 + - - -
4A ALA* 1.3 76.8 - - - +
6A PHE* 1.3 57.3 + - - -
25A LEU* 4.4 6.7 - - - -
26A ALA 3.4 10.8 - - - -
27A THR* 4.3 6.5 - - - -
123A PRO 3.6 0.2 - - - -
124A VAL* 2.7 52.8 + - - +
146A TYR* 3.4 13.5 - - - -
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Residues in contact with PHE 6 (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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5A GLY* 1.3 74.7 - - - -
7A ILE* 1.3 73.9 + - - +
8A LEU* 3.4 5.6 + - + +
25A LEU* 4.2 2.6 - - - +
26A ALA* 2.8 35.7 + - - +
122A SER* 3.2 28.7 - - - -
123A PRO* 3.7 12.1 - - + -
146A TYR* 3.7 14.8 - - + -
147A ARG* 4.1 11.4 - - - -
148A PRO* 3.5 38.6 - - + -
353A LEU* 3.5 37.2 - - + -
356A ALA* 4.8 0.2 - - + -
357A THR* 3.5 22.2 - - - -
363A VAL* 3.6 17.9 - - + -
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Residues in contact with ILE 7 (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 PHE* 1.3 88.2 - - - +
8A LEU* 1.3 62.3 + - - +
9A THR 3.8 16.2 - - - +
10A ARG* 3.7 33.8 + - + +
23A PHE* 4.3 7.0 - - + -
24A TRP 3.7 5.6 - - - +
25A LEU* 3.7 18.8 - - + -
115A LEU* 3.8 33.2 - - + -
120A ILE* 4.3 0.2 - - + -
121A THR 4.1 7.9 - - - +
122A SER* 3.0 19.9 + - - +
124A VAL* 3.7 24.7 - - + -
140A LEU* 4.4 5.2 - - + -
363A VAL* 4.6 4.0 + - - +
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Residues in contact with LEU 8 (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 PHE* 4.1 9.2 - - + +
7A ILE* 1.3 80.9 - - - +
9A THR* 1.3 65.1 + - + +
10A ARG* 3.8 9.4 + - - -
24A TRP 2.8 16.3 + - - +
25A LEU 4.9 1.3 - - - -
26A ALA* 4.0 28.7 - - + +
150A LEU* 4.3 10.5 - - + -
218A ASP* 3.9 20.0 - - + +
248A ARG* 3.4 15.9 - - - +
271A GLY 3.3 26.9 - - - +
272A ARG* 4.7 0.2 - - - -
273A LEU* 3.3 48.1 - - + +
353A LEU* 5.9 0.4 - - + -
362A PRO* 5.0 5.0 - - - +
363A VAL 5.2 1.2 + - - -
364A ASP* 5.1 0.9 - - - +
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Residues in contact with THR 9 (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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7A ILE* 3.8 6.3 - - - +
8A LEU* 1.3 83.5 - - - +
10A ARG* 1.3 65.7 + - - +
11A HIS* 2.6 32.8 - - - +
23A PHE* 3.5 4.2 - - - -
24A TRP* 3.1 27.6 + - - +
269A ALA 4.0 4.5 - - - +
271A GLY* 2.9 26.0 + - - +
272A ARG 3.4 28.7 - - - +
273A LEU* 5.1 0.7 - - + -
364A ASP* 6.0 0.2 - - - +
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Residues in contact with ARG 10 (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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7A ILE* 3.7 22.6 + - + +
8A LEU 3.8 11.7 + - - -
9A THR* 1.3 75.9 - - - +
11A HIS* 1.3 75.8 + - - +
22A SER 3.8 4.0 - - - -
23A PHE* 3.8 16.4 - - + -
111A PRO* 3.9 16.8 - - + -
112A GLU* 4.3 22.9 - - - +
115A LEU* 3.6 16.7 - - - +
121A THR 3.6 22.0 + - - -
122A SER* 3.8 13.5 + - - -
360A GLY 4.5 6.9 + - - -
361A LEU 4.3 4.8 + - - -
362A PRO* 3.7 44.0 - - - +
363A VAL 5.2 0.2 - - - +
375A HIS* 6.2 0.2 + - - -
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Residues in contact with HIS 11 (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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9A THR* 2.6 41.4 + - - -
10A ARG* 1.3 83.8 + - - +
12A TRP* 1.3 66.5 + - - +
21A VAL* 3.5 1.0 - - - -
22A SER* 2.9 49.5 + - - +
24A TRP* 3.5 21.6 - + - -
111A PRO* 3.5 11.9 - - - +
270A LYS* 3.6 34.1 - - + +
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Residues in contact with TRP 12 (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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11A HIS* 1.3 79.3 - - - +
13A ARG* 1.3 72.2 + - - +
14A ASP* 3.7 19.5 - - - -
19A THR* 4.2 3.8 - - + -
20A GLU 3.1 12.3 - - - +
21A VAL* 4.3 1.8 - - + -
86A HIS* 3.6 43.3 - + + -
87A ARG* 3.9 37.5 - - + -
109A ARG* 4.2 19.4 - - + +
110A PRO* 3.8 21.1 - - + +
111A PRO* 3.4 33.7 - - + -
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Residues in contact with ARG 13 (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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12A TRP* 1.3 86.5 - - - +
14A ASP* 1.3 64.8 + - - +
15A THR* 3.7 18.4 + - + +
19A THR* 3.6 0.6 - - - -
20A GLU* 2.9 72.8 + - + +
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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