Contacts of the strand formed by residues 6 - 14 (chain A) in PDB entry 4P5K
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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA* 4.5 5.6 - - + -
5A HIS* 1.3 81.1 - - - +
7A SER* 1.3 61.8 + - - +
8A THR* 3.5 25.1 + - + +
25A GLU* 3.8 1.4 - - - +
26A PHE* 3.7 2.1 - - - -
27A ASP* 2.9 41.0 + - - +
28A GLU* 4.6 4.2 + - - +
14B GLU* 4.7 0.4 - - + -
15B CYS 3.3 6.1 - - - +
16B TYR* 3.7 39.0 - - + +
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Residues in contact with SER 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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5A HIS* 4.3 0.7 - - - +
6A VAL* 1.3 70.8 + - - +
8A THR* 1.3 58.9 + - - +
9A TYR* 5.9 0.2 - - - -
24A PHE* 3.8 25.4 - - - -
25A GLU 3.5 4.9 - - - -
26A PHE* 3.6 24.8 - - - -
13B GLN 3.6 1.9 - - - +
14B GLU* 3.4 0.9 - - - -
15B CYS* 2.6 48.6 + - - +
80B ASN* 6.1 2.9 - - - -
81B TYR* 5.2 11.1 - - - -
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Residues in contact with THR 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 VAL* 3.5 30.7 - - + +
7A SER* 1.3 81.8 - - - +
9A TYR* 1.3 65.2 + - - +
10A ALA* 3.7 6.2 + - - +
24A PHE* 3.4 6.4 - - - -
25A GLU* 3.2 53.4 + - + +
12B ARG* 4.8 5.6 + - - -
13B GLN 3.2 3.8 - - - -
14B GLU* 3.5 28.7 - - + -
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Residues in contact with TYR 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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8A THR* 1.3 73.8 + - - +
10A ALA* 1.3 59.6 + - - +
11A ALA* 4.3 0.4 - - + -
22A PHE* 3.8 28.0 - + + -
23A MET 3.4 13.9 - - - +
24A PHE* 3.8 28.4 - + + -
32A PHE* 3.9 19.5 - + - -
54A PHE* 3.6 22.8 - + - -
-23B PHE* 4.2 3.5 - - - +
-22B ASP 2.4 34.4 + - - -
-21B THR* 4.6 3.8 - - + -
-20B GLN 5.4 0.9 - - - -
-18B PHE* 4.6 3.2 - - + -
11B GLY 4.0 0.3 - - - +
12B ARG* 3.3 5.4 - - - +
13B GLN* 2.9 62.4 + - - +
76B MET* 4.1 20.4 - - + -
80B ASN* 3.8 7.6 + - - -
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Residues in contact with ALA 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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8A THR* 3.7 6.8 + - - +
9A TYR* 1.3 75.0 - - - +
11A ALA* 1.3 61.3 + - - +
12A PHE* 6.2 0.4 - - - -
21A GLU* 4.2 1.0 - - - +
22A PHE* 4.1 0.6 - - - -
23A MET* 3.0 40.0 + - + +
25A GLU* 5.8 0.7 - - + -
139A PRO* 3.9 34.3 - - + -
11B GLY 3.5 8.3 - - - +
12B ARG* 4.3 11.2 - - - +
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Residues in contact with ALA 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 TYR* 6.4 0.2 - - + -
10A ALA* 1.3 76.5 - - - +
12A PHE* 1.3 64.5 + - - +
21A GLU 3.1 14.4 - - - +
22A PHE* 4.0 22.4 - - + -
62A ASN* 5.6 0.2 - - + -
63A ILE* 4.4 2.9 - - + -
66A LEU* 3.6 20.3 - - + +
-18B PHE* 4.3 13.0 - - + -
10B GLN* 3.4 4.7 - - - +
11B GLY 3.0 30.8 + - - +
12B ARG* 5.6 0.3 + - - -
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Residues in contact with PHE 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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10A ALA 6.2 0.4 - - - -
11A ALA* 1.3 77.6 - - - +
13A VAL* 1.3 71.4 + - - +
14A GLN* 3.7 9.6 - - - -
18A PRO* 3.5 27.4 - - + -
20A GLY* 3.2 3.9 - - - -
21A GLU* 2.9 74.2 + - + +
63A ILE* 4.6 2.1 - - - +
66A LEU* 4.2 1.8 - - - -
115A PRO* 4.0 15.0 - - + -
137A PHE* 3.9 10.3 - + + -
145A PHE* 3.5 33.7 - + + -
8B LEU* 4.1 22.0 - - + -
9B PHE 3.3 12.3 - - - +
10B GLN* 4.2 6.1 - - + +
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Residues in contact with VAL 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 PHE* 1.3 82.9 - - - +
14A GLN* 1.3 64.4 + - - +
19A THR* 3.4 13.7 - - + +
20A GLY* 4.4 0.7 - - - -
63A ILE* 4.1 27.4 - - + +
66A LEU* 3.7 28.3 - - + +
67A ASN* 3.4 33.0 - - - +
70A LEU* 3.5 18.3 - - + +
8B LEU* 3.3 2.1 - - - +
9B PHE* 3.0 34.8 + - + +
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Residues in contact with GLN 14 (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 PHE* 3.7 10.4 - - + -
13A VAL* 1.3 76.8 - - - +
15A THR* 1.3 64.9 + - - +
16A HIS 3.4 19.0 + - - +
18A PRO* 3.0 24.6 + - - +
19A THR* 3.1 25.9 + - - +
67A ASN* 5.3 1.1 + - - +
70A LEU* 3.9 7.2 - - - -
115A PRO* 3.2 32.5 + - - +
116A VAL* 3.7 7.8 - - - +
6B ASN* 2.8 23.7 - - - +
7B TYR 3.1 16.8 - - - +
8B LEU* 3.4 23.3 - - + +
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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