Contacts of the strand formed by residues 8 - 17 (chain E) 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 LEU 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.1 12.3 - - + -
13D VAL 3.6 10.3 - - - +
14D GLN* 3.8 14.1 - - + +
70D LEU* 3.6 6.6 - - - +
113D PHE* 4.1 18.4 - - + -
114D PRO* 5.1 0.4 - - + -
115D PRO* 3.6 35.7 - - + -
145D PHE* 4.5 2.5 - - + -
6E ASN* 5.0 1.8 - - - +
7E TYR* 1.3 79.3 - - - +
9E PHE* 1.3 63.6 + - - +
10E GLN* 3.2 40.6 - - + +
30E TYR* 3.5 9.4 - - - -
31E ASN* 2.7 44.1 + - - +
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Residues in contact with PHE 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.1 4.7 - - - +
13D VAL* 3.0 33.1 + - - +
66D LEU* 3.5 49.1 - - + +
69D ASN* 3.6 32.5 - - + -
70D LEU* 3.6 16.1 - - + +
73D LEU* 3.9 12.3 - - + -
-15E ILE* 4.2 6.1 - - + -
8E LEU* 1.3 80.7 - - - +
10E GLN* 1.3 68.0 - - - +
11E GLY* 5.3 0.4 - - - -
28E TYR* 4.1 19.7 - + + -
29E ILE 3.4 20.0 - - - -
30E TYR* 4.4 10.5 - + - -
35E PHE* 3.8 16.4 - + - -
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Residues in contact with GLN 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA 3.1 13.0 - - - +
12D PHE* 4.0 8.3 - - + -
66D LEU* 4.8 0.7 - - - -
113D PHE* 4.1 2.2 - - - -
143D TYR* 3.4 35.4 + - - +
144D SER 5.0 0.2 - - - +
145D PHE* 3.9 12.5 - - + -
8E LEU* 3.2 22.5 - - + +
9E PHE* 1.3 80.8 - - - +
11E GLY* 1.3 60.4 + - - +
12E ARG* 2.8 34.6 + - - +
29E ILE* 2.9 44.9 + - + +
32E ARG 3.4 24.4 - - - +
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Residues in contact with GLY 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA 2.9 23.9 + - - +
66D LEU* 4.4 4.6 - - - +
-18E PHE* 3.6 21.8 - - - -
9E PHE* 5.3 0.2 - - - -
10E GLN* 1.3 75.8 - - - +
12E ARG* 1.3 79.6 + - - -
27E ARG 3.1 11.9 - - - -
28E TYR* 4.9 0.4 - - - -
29E ILE* 4.3 1.6 - - - -
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Residues in contact with ARG 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 5.0 4.5 - - - -
9D TYR 3.3 4.3 - - - -
10D ALA* 3.6 17.9 - - - +
11D ALA 5.5 0.8 + - - -
25D GLU* 6.1 0.7 - - - -
139D PRO* 3.5 27.3 - - - +
140D ARG 2.8 30.3 + - - -
141D THR* 4.7 1.6 - - - +
143D TYR* 4.0 13.6 - - + +
144D SER 5.5 0.4 + - - -
145D PHE* 5.2 2.2 - - - -
-18E PHE* 3.8 1.0 - - - -
10E GLN* 2.8 36.2 + - - +
11E GLY* 1.3 83.7 + - - -
13E GLN* 1.3 61.6 + - - +
14E GLU* 3.2 34.1 - - + +
25E LEU 4.0 0.2 - - - -
26E GLU* 3.0 12.3 - - - +
27E ARG* 2.9 44.1 + - + -
29E ILE* 4.2 6.3 - - + +
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Residues in contact with GLN 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D SER 3.9 1.2 - - - +
8D THR* 3.4 2.9 - - - -
9D TYR* 2.8 58.3 + - + +
22D PHE* 5.2 0.7 - - - -
62D ASN* 4.0 4.0 + - - -
-21E THR* 4.2 3.1 - - - +
-20E GLN* 3.2 37.9 + - - +
-18E PHE* 3.7 33.4 - - + +
12E ARG* 1.3 75.8 - - - +
14E GLU* 1.3 60.9 + - - +
15E CYS* 5.1 1.7 - - - -
24E PHE* 4.0 15.7 - - + -
25E LEU 3.5 3.1 - - - -
26E GLU* 3.0 28.6 + - + +
76E MET* 4.4 10.0 - - + +
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Residues in contact with GLU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 5.4 0.4 - - - -
8D THR* 3.5 24.9 - - + -
12E ARG* 3.2 20.8 - - + +
13E GLN* 1.3 73.1 - - - +
15E CYS* 1.3 62.2 + - - +
16E TYR* 2.4 42.0 + - + -
23E ARG 3.6 1.2 - - - +
24E PHE* 3.3 7.7 - - - -
25E LEU* 2.5 44.1 + - + +
27E ARG* 2.7 45.4 + - - -
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Residues in contact with CYS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D HIS 3.8 0.9 - - - +
6D VAL* 3.4 3.0 - - - -
7D SER* 2.9 50.7 + - - +
13E GLN 5.1 1.1 - - - -
14E GLU* 1.3 75.3 - - - +
16E TYR* 1.3 63.4 + - - +
22E GLN* 4.1 6.9 - - - +
23E ARG 3.5 3.8 - - - -
24E PHE* 4.1 0.7 - - - -
76E MET* 4.0 19.5 - - - -
77E CYS* 2.1 54.5 - - + +
80E ASN* 5.5 3.1 - - - -
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Residues in contact with TYR 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ILE* 3.5 49.2 - - + +
2D LYS 5.1 0.7 - - - +
3D ALA* 3.7 12.1 - - + -
5D HIS 3.4 4.5 - - - -
6D VAL* 3.5 34.1 - - + +
14E GLU* 2.4 37.2 + - + -
15E CYS* 1.3 73.5 - - - +
17E ALA* 1.3 60.6 + - - +
18E PHE* 4.0 3.9 + - + +
21E THR 3.7 0.5 - - - +
22E GLN* 3.4 6.6 - - - -
23E ARG* 2.7 56.2 + - + +
25E LEU* 3.3 27.6 - - + -
27E ARG* 4.0 3.6 + - - -
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Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ALA* 3.6 1.0 - - - -
4D ASP* 2.9 30.2 + - + +
5D HIS* 2.8 20.6 + - + +
15E CYS 4.0 0.4 + - - -
16E TYR* 1.3 70.7 - - - +
18E PHE* 1.3 62.4 + - - +
21E THR 3.5 6.1 - - - +
22E GLN* 3.5 13.6 + - - +
81E TYR* 3.3 42.4 - - + +
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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