Contacts of the strand formed by residues 15 - 23 (chain T) in PDB entry 4QAE
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 HIS 15 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D GLU 5.0 0.2 + - - -
75D LYS* 4.0 11.7 - - - +
76D CYS* 3.8 24.5 + - - -
174D GLN* 3.4 4.5 - - - -
175D CYS* 4.9 0.4 - - - -
202D MPD 3.4 27.8 - - + -
10T CYS 3.7 1.6 - - - -
12T GLY* 3.1 18.9 + - - -
13T CYS 3.2 0.6 - - - -
14T CYS* 1.3 93.3 - - - +
16T ARG* 1.3 67.5 + - - +
17T SER 3.3 0.9 + - - -
18T LYS* 3.1 36.3 + - + +
19T CYS 4.1 1.6 + - - -
20T GLY* 3.5 29.9 + - - -
21T MET 4.4 2.4 + - - -
22T CYS* 3.7 13.4 - - - -
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Residues in contact with ARG 16 (chain T).
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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43A ARG 5.2 7.5 + - - -
44A GLU* 5.6 3.8 + - - +
45A ASP 6.1 0.6 - - - +
46A LYS* 2.8 42.4 + - - +
174D GLN* 2.9 31.8 + - - +
5E SER* 5.7 1.8 + - - -
40E GLU* 3.5 22.7 - - + +
42E LEU* 3.3 33.9 - - - +
44E GLU* 2.8 31.5 + - - -
12T GLY* 4.5 2.0 - - - -
13T CYS 5.0 1.8 + - - -
15T HIS* 1.3 71.1 - - - +
17T SER* 1.3 65.0 + - - +
18T LYS* 3.1 1.2 + - - +
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Residues in contact with SER 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS* 4.1 1.8 - - - -
40E GLU 2.9 18.5 + - - -
41E VAL* 4.0 11.9 - - - +
42E LEU* 2.9 29.9 + - - +
44E GLU* 2.8 41.4 + - - +
49E MET* 3.7 19.2 - - - +
12T GLY* 4.4 0.6 - - - -
15T HIS 3.3 1.2 + - - -
16T ARG* 1.3 75.5 + - - +
18T LYS* 1.3 66.4 + - - +
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Residues in contact with LYS 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS* 3.9 13.9 - - - +
73D ALA 3.8 18.5 + - - -
74D GLU* 4.4 23.1 - - + +
202D MPD 3.9 24.7 - - + +
44E GLU* 6.5 0.9 - - - -
47E ASP* 2.9 35.3 + - - -
49E MET* 4.8 5.9 - - + +
12T GLY 3.0 23.1 + - - -
15T HIS* 3.1 29.1 + - + -
16T ARG 3.1 3.1 + - - +
17T SER* 1.3 85.8 + - - +
19T CYS* 1.3 65.5 + - - +
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Residues in contact with CYS 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D GLU 4.7 6.8 - - - +
36E LEU* 3.8 12.8 - - - -
41E VAL* 5.3 0.4 - - - -
49E MET* 4.0 10.4 - - - +
52E TRP* 3.8 14.6 - - + -
70E MET* 3.3 32.2 - - + +
9T PHE* 3.6 15.0 - - + -
10T CYS 3.2 3.8 - - - -
11T CYS* 2.1 46.7 - - - -
15T HIS* 3.9 4.0 + - - -
18T LYS* 1.3 78.2 - - - +
20T GLY* 1.3 58.4 - - - +
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Residues in contact with GLY 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LYS* 6.1 3.1 - - - -
79E LEU* 3.8 9.2 - - - -
9T PHE* 3.6 19.3 - - - -
10T CYS* 2.9 31.7 + - - +
15T HIS* 3.5 11.3 - - - -
19T CYS* 1.3 74.9 - - - +
21T MET* 1.3 64.1 + - - -
22T CYS* 3.5 2.6 + - - -
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Residues in contact with MET 21 (chain T).
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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75D LYS* 6.0 5.9 - - - +
76D CYS* 4.3 7.4 + - - +
78D TYR* 3.6 15.8 - - + -
79E LEU* 4.0 35.5 - - + +
80E PHE 5.0 12.6 - - - +
81E GLN* 6.1 0.9 - - + -
7T CYS* 4.1 17.9 - - + +
8T ILE* 3.4 29.4 - - - +
9T PHE* 3.8 20.2 - - + +
14T CYS* 3.8 3.6 - - - -
15T HIS* 4.4 3.0 + - - -
20T GLY* 1.3 70.7 - - - -
22T CYS* 1.3 63.3 + - - +
23T CYS* 5.2 3.8 - - - -
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Residues in contact with CYS 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D TYR* 3.6 0.7 - - - -
127E TRP* 3.6 25.0 - - + -
6T ILE 4.0 0.2 - - - +
7T CYS* 3.2 1.0 - - - -
8T ILE* 2.8 40.0 + - + +
10T CYS* 4.2 3.1 - - - -
12T GLY 3.7 0.4 - - - -
13T CYS* 3.7 11.2 - - + -
14T CYS* 2.1 54.7 - - - -
15T HIS* 3.7 13.7 - - - -
20T GLY 4.0 3.8 - - - -
21T MET* 1.3 75.0 - - - +
23T CYS* 1.3 62.4 + - - +
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Residues in contact with CYS 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D THR* 6.1 1.3 - - + -
78D TYR* 3.1 58.4 + - + -
80D PHE* 5.4 1.3 - - + -
127E TRP* 3.3 11.1 - - - -
5T PRO* 5.0 7.6 - - + -
6T ILE 3.2 4.3 - - - +
7T CYS* 2.0 44.9 - - - -
21T MET* 5.2 4.0 - - - -
22T CYS* 1.3 74.5 - - - +
24T LYS* 1.3 68.5 + - - +
25T THR* 3.5 4.7 + - - +
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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