Contacts of the strand formed by residues 7 - 17 (chain B) in PDB entry 1K2D
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 PHE 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLN* 3.0 18.5 - - - +
15A SER* 3.1 29.1 + - - +
16A PRO* 5.3 0.9 - - + -
70A LEU* 4.0 15.7 - - + +
74A THR* 4.0 14.4 - - + +
79A SER* 3.9 22.4 - - - -
80A THR 3.1 31.6 - - - -
81A PRO* 3.6 15.0 - - + -
5B ARG* 3.7 31.9 - - - -
6B HIS* 1.3 77.1 - - - +
8B VAL* 1.3 63.8 + - - +
32B TYR* 3.7 12.1 - - - +
33B ASN* 3.6 5.6 - - - -
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Residues in contact with VAL 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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12A VAL* 4.0 14.4 - - + -
13A TYR 3.1 22.0 - - - +
14A GLN* 3.4 28.3 - - + +
70A LEU* 3.8 2.7 - - - -
82A ALA* 4.7 3.8 - - + -
113A PHE* 4.9 3.4 - - + -
114A PRO* 4.2 14.1 - - + -
115A PRO* 4.6 6.3 - - + -
7B PHE* 1.3 82.7 - - - +
9B VAL* 1.3 79.1 + - - +
10B GLN* 4.9 2.9 - - + -
32B TYR* 3.4 11.6 - - - -
33B ASN* 2.5 47.8 + - - +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.6 0.4 - - - -
12A VAL* 3.6 0.7 - - - -
13A TYR* 3.0 53.0 + - + +
66A GLY* 3.6 7.4 - - - +
69A ASN* 4.0 8.3 - - + +
70A LEU* 3.5 40.4 - - + +
73A LEU* 4.4 4.9 - - + -
8B VAL* 1.3 81.9 - - - +
10B GLN* 1.3 70.5 + - - +
31B ILE 3.3 12.6 - - - +
32B TYR* 4.2 9.4 - - + -
37B TYR* 5.2 1.3 - - - +
4P TYR* 4.0 13.9 - - + +
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Residues in contact with GLN 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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11A VAL 3.3 7.2 - - - +
12A VAL* 4.4 8.4 - - + +
113A PHE* 4.2 4.6 - - - -
139A VAL* 4.6 0.2 - - - +
143A TYR* 3.2 24.8 + - - +
145A PHE* 3.1 33.1 - - + -
8B VAL* 4.9 3.3 - - + +
9B VAL* 1.3 81.1 - - - +
11B PHE* 1.3 60.1 + - - +
12B GLN* 3.0 28.5 + - + +
30B TYR* 3.8 1.7 - - - -
31B ILE* 2.8 54.4 + - + +
33B ASN 3.1 24.2 + - - +
4P TYR* 4.1 6.9 + - - -
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.3 23.1 - - - -
10A ILE* 3.3 1.9 - - - +
11A VAL* 2.8 34.7 + - + -
62A ASN* 5.0 0.2 - - - -
10B GLN* 1.3 73.9 - - - +
12B GLN* 1.3 60.2 + - - +
13B PRO* 3.2 22.8 - - + +
28B THR* 3.1 37.9 - - + -
29B ARG 3.2 13.5 - - - -
30B TYR* 3.6 10.5 - + - -
2P SER* 3.1 24.5 - - - -
3P GLN 3.5 16.2 - - - -
4P TYR* 3.2 55.0 - + + -
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.4 7.4 - - + -
139A VAL* 3.4 39.4 - - + +
140A ASN 4.2 6.2 + - - +
143A TYR* 3.4 30.9 - - - +
10B GLN* 3.0 28.3 + - + +
11B PHE* 1.3 76.8 - - - +
13B PRO* 1.3 60.6 - - - +
14B PHE* 3.0 42.6 - - + -
28B THR* 4.7 0.2 - - - -
29B ARG* 3.0 37.8 + - + -
31B ILE* 4.2 4.4 - - + +
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Residues in contact with PRO 13 (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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7A GLY 4.3 0.2 - - - -
8A SER* 2.9 34.3 + - - -
9A TYR 3.6 40.8 - - - +
10A ILE* 3.9 9.2 - - + +
11B PHE* 3.2 24.5 - - + +
12B GLN* 1.3 83.1 - - - +
14B PHE* 1.3 59.7 + - - +
15B CYS* 6.1 0.9 - - - -
26B TYR* 4.9 1.1 - - + -
27B VAL 3.7 7.2 - - - +
28B THR* 4.3 6.3 - - - +
2P SER* 3.8 26.7 - - - +
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Residues in contact with PHE 14 (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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6A VAL* 4.0 13.7 - - + -
7A GLY 3.4 3.4 - - - -
8A SER* 3.5 19.5 - - - -
139A VAL* 4.7 9.2 - - + -
140A ASN 5.9 0.2 - - - -
143A TYR* 5.7 0.4 - + - -
12B GLN* 3.0 62.6 - - + -
13B PRO* 1.3 71.3 - - - +
15B CYS* 1.3 61.6 + - - +
16B TYR* 3.3 36.5 - + + -
25B ARG 3.5 5.0 - - - +
26B TYR* 3.7 1.9 - - - -
27B VAL* 3.0 45.7 + - + +
29B ARG* 3.8 25.8 - - + -
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Residues in contact with CYS 15 (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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6A VAL* 3.5 1.3 - - - -
7A GLY 2.6 26.3 + - - +
9A TYR* 3.5 22.2 - - + -
13B PRO 6.1 0.7 - - - -
14B PHE* 1.3 72.6 - - - +
16B TYR* 1.3 60.4 + - - +
17B PHE* 2.9 36.4 - - + -
24B ILE* 5.5 0.4 - - - -
25B ARG 4.3 1.8 - - - -
26B TYR* 4.7 4.3 - - - +
78B VAL* 4.5 3.6 - - - -
79B CYS* 2.0 57.2 - - + -
2P SER* 5.1 1.3 - - - -
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Residues in contact with TYR 16 (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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1A ILE* 3.6 56.4 - - + +
2A GLU 5.4 0.4 - - - +
3A ALA* 3.8 14.4 - - + -
5A HIS 3.7 1.6 - - - -
6A VAL* 3.8 26.6 - - + +
14B PHE* 3.3 43.0 - + + -
15B CYS* 1.3 69.7 - - - +
17B PHE* 1.3 61.7 + - - +
18B THR* 5.8 0.2 - - - +
23B ARG 3.3 6.6 - - - +
24B ILE* 3.4 3.1 - - - +
25B ARG* 3.0 54.4 + - + +
27B VAL* 4.8 11.2 - - + -
29B ARG* 4.7 7.4 + - - -
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Residues in contact with PHE 17 (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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3A ALA* 3.1 4.2 - - - +
4A ASP* 2.8 30.2 + - - -
5A HIS* 3.0 33.0 + - + -
7A GLY 3.9 8.7 - - - -
9A TYR* 4.1 16.8 - - - -
26A PHE* 4.2 3.8 - + - -
15B CYS* 2.9 47.1 - - + -
16B TYR* 1.3 75.3 - - - +
18B THR* 1.3 59.9 + - - +
20B GLY 3.8 11.0 - - - +
21B THR* 4.7 0.9 - - + -
23B ARG 4.3 0.9 - - - -
24B ILE* 4.2 21.3 - - + +
79B CYS* 4.2 19.1 - - + -
80B ARG 4.6 1.1 - - - -
83B TYR* 3.4 47.3 - + + -
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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