Contacts of the strand formed by residues 15 - 23 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LYS* 4.0 10.5 - - - -
76A CYS* 3.7 21.9 + - - -
174A GLN* 3.2 4.5 - - - -
201A MPD 3.4 29.6 - - + -
10R CYS 3.7 4.3 - - - -
12R GLY* 3.1 20.5 + - - +
13R CYS 3.3 0.8 - - - -
14R CYS* 1.3 95.8 - - - +
16R ARG* 1.3 66.8 + - - +
18R LYS* 3.1 36.9 + - + +
19R CYS 4.1 1.2 + - - -
20R GLY* 3.5 31.5 + - - -
21R MET 4.2 2.0 + - - -
22R CYS* 3.7 9.3 - - - -
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Residues in contact with ARG 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 2.8 35.6 + - - +
40C GLU* 3.5 23.1 - - + +
42C LEU* 3.9 26.1 - - + +
44C GLU* 4.6 7.3 + - - -
43D ARG 5.1 8.9 + - - -
44D GLU* 5.5 4.2 + - - -
46D LYS* 2.8 35.1 + - - +
164D ASN* 6.0 2.0 - - - +
12R GLY* 4.4 3.1 - - - -
13R CYS 4.8 1.8 + - - -
15R HIS* 1.3 72.6 - - - +
17R SER* 1.3 71.4 + - - +
18R LYS* 3.2 1.6 + - - +
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Residues in contact with SER 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU 2.9 16.7 + - - -
41C VAL* 4.0 12.3 - - - +
42C LEU* 2.9 26.6 + - - +
44C GLU* 2.6 42.4 + - - +
49C MET* 3.6 20.0 - - - +
46D LYS* 4.4 2.0 - - - -
12R GLY* 4.5 0.4 - - - -
15R HIS 3.3 0.6 + - - -
16R ARG* 1.3 77.3 - - - +
18R LYS* 1.3 66.8 + - - +
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Residues in contact with LYS 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 3.8 20.6 + - - -
74A GLU* 4.4 24.4 - - - +
201A MPD 4.3 9.2 - - + +
44C GLU* 6.5 0.9 - - - -
47C ASP* 2.7 35.2 + - - +
49C MET* 4.8 4.4 - - + +
46D LYS* 4.1 20.2 - - - +
11R CYS* 4.2 0.2 - - - -
12R GLY 3.0 23.6 + - - +
15R HIS* 3.1 29.9 + - + +
16R ARG 3.2 9.6 - - - +
17R SER* 1.3 85.0 - - - +
19R CYS* 1.3 64.2 + - - +
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Residues in contact with CYS 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU 4.8 6.4 - - - +
36C LEU* 3.7 17.3 - - - -
49C MET* 4.2 9.1 - - - +
52C TRP* 3.8 8.7 - - + -
70C MET* 3.5 31.0 - - + +
9R PHE* 3.5 15.9 - - + -
10R CYS 3.2 4.5 - - - -
11R CYS* 2.1 48.2 - - - -
15R HIS* 3.9 3.0 + - - -
18R LYS* 1.3 78.4 - - - +
20R GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 5.9 4.5 - - - -
79C LEU* 4.0 8.5 - - - -
8R ILE 3.6 0.2 - - - +
9R PHE* 3.4 16.3 - - - -
10R CYS 2.9 32.5 + - - +
15R HIS* 3.5 13.8 - - - -
19R CYS* 1.3 76.0 - - - +
21R MET* 1.3 64.4 + - - -
22R CYS* 3.6 0.9 + - - -
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Residues in contact with MET 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 5.8 2.3 - - - +
76A CYS* 4.2 7.9 + - - +
78A TYR* 3.7 15.8 - - + -
79C LEU* 3.9 37.4 - - + +
80C PHE 4.8 13.7 - - - +
81C GLN* 5.8 0.9 - - + -
7R CYS* 4.1 16.4 - - + +
8R ILE* 3.5 28.7 - - - +
9R PHE* 3.9 20.2 - - + +
14R CYS* 3.7 8.3 - - - -
15R HIS* 4.2 2.6 + - - -
20R GLY* 1.3 71.0 - - - -
22R CYS* 1.3 59.5 - - - +
23R CYS* 5.3 3.6 - - - -
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Residues in contact with CYS 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.6 0.7 - - - -
127C TRP* 3.5 30.0 - - + -
7R CYS* 3.2 0.9 - - - -
8R ILE* 2.9 36.2 + - + +
10R CYS* 4.2 2.9 - - - -
12R GLY 3.8 0.2 - - - -
13R CYS* 3.8 9.2 - - + -
14R CYS* 2.1 54.5 - - - -
15R HIS* 3.7 13.7 - - - -
20R GLY 4.2 3.8 - - - -
21R MET* 1.3 75.2 - - - +
23R CYS* 1.3 62.3 + - - +
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Residues in contact with CYS 23 (chain R).
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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67A THR* 6.0 0.9 - - + -
78A TYR* 3.2 49.4 + - + -
80A PHE* 5.1 2.5 - - + -
127C TRP* 3.3 11.1 - - - -
5R PRO* 4.8 7.9 - - + -
6R ILE 3.4 4.7 - - - +
7R CYS* 2.0 45.5 - - - -
21R MET* 5.3 4.0 - - - -
22R CYS* 1.3 74.5 - - - +
24R LYS* 1.3 69.3 + - - +
25R THR* 3.3 14.3 + - + +
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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