Contacts of the strand formed by residues 15 - 23 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75F LYS* 3.9 11.5 - - - -
76F CYS* 3.7 23.4 + - - -
174F GLN* 3.2 5.4 - - - -
203F MPD 3.4 27.6 - - + -
10S CYS 3.8 1.1 - - - -
12S GLY* 3.1 19.3 + - - +
13S CYS 3.3 1.0 - - - -
14S CYS* 1.3 94.6 - - - +
16S ARG* 1.3 66.3 + - - +
18S LYS* 3.1 36.7 + - + +
19S CYS 4.2 1.2 + - - -
20S GLY* 3.5 30.9 + - - -
21S MET 4.3 2.2 + - - -
22S CYS* 3.7 12.7 - - - -
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Residues in contact with ARG 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG 4.8 11.1 + - - -
44C GLU* 5.0 7.7 + - - +
45C ASP* 5.8 2.6 - - - +
46C LYS* 2.6 35.2 + - - +
164C ASN* 5.7 4.8 - - - +
40D GLU* 3.6 19.5 - - + +
42D LEU* 3.7 27.5 - - + +
44D GLU* 4.7 8.7 + - - -
174F GLN* 2.8 32.9 + - - +
203F MPD 4.5 0.2 - - - +
12S GLY* 4.5 2.7 - - - -
13S CYS 5.0 1.6 + - - -
15S HIS* 1.3 71.9 - - - +
17S SER* 1.3 64.6 + - - +
18S LYS* 3.1 2.3 + - - +
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Residues in contact with SER 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS* 4.1 2.5 - - - -
40D GLU 2.9 16.5 + - - -
41D VAL* 4.0 13.2 - - - +
42D LEU* 3.0 25.7 + - - +
44D GLU* 2.7 42.1 + - - +
49D MET* 3.7 19.9 - - - +
12S GLY* 4.6 0.4 - - - -
15S HIS 3.4 0.8 + - - -
16S ARG* 1.3 76.8 - - - +
18S LYS* 1.3 67.5 + - - +
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Residues in contact with LYS 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS* 4.0 20.2 - - - +
44D GLU* 6.4 0.9 - - - -
47D ASP* 2.9 33.3 + - - -
49D MET* 5.0 3.3 - - + +
73F ALA 3.7 21.1 + - - -
74F GLU* 4.4 24.5 - - - +
203F MPD 4.2 10.5 - - + +
11S CYS* 4.3 0.2 - - - -
12S GLY 2.9 24.3 + - - -
15S HIS* 3.1 30.1 + - + +
16S ARG 3.1 9.6 + - - +
17S SER* 1.3 86.1 - - - +
19S CYS* 1.3 64.7 + - - +
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Residues in contact with CYS 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.7 18.6 - - - -
41D VAL* 5.3 0.4 - - - -
49D MET* 4.1 9.3 - - - +
52D TRP* 3.8 9.2 - - + -
70D MET* 3.5 30.7 - - + +
74F GLU 4.8 6.2 - - - +
9S PHE* 3.6 15.7 - - + -
10S CYS 3.2 5.2 - - - -
11S CYS* 2.1 46.7 - - - -
15S HIS* 3.9 2.5 + - - -
18S LYS* 1.3 77.5 - - - +
20S GLY* 1.3 57.5 + - - +
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Residues in contact with GLY 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 3.9 16.2 - - - -
75F LYS* 5.9 4.3 - - - -
8S ILE 3.6 0.2 - - - +
9S PHE* 3.4 11.0 - - - -
10S CYS 2.9 31.6 + - - +
15S HIS* 3.5 12.7 - - - -
19S CYS* 1.3 75.5 - - - +
21S MET* 1.3 63.7 + - - -
22S CYS* 3.6 2.1 + - - -
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Residues in contact with MET 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 3.9 35.3 - - + +
80D PHE 4.9 11.7 - - - +
81D GLN* 6.1 0.7 - - + -
75F LYS* 5.9 3.2 - - - +
76F CYS* 4.3 8.2 + - - +
78F TYR* 3.7 14.9 - - + -
7S CYS* 4.0 17.7 - - + +
8S ILE* 3.5 33.7 - - - +
9S PHE* 3.8 19.3 - - + +
14S CYS* 3.8 7.1 - - - -
15S HIS* 4.3 3.1 + - - -
20S GLY* 1.3 71.0 - - - -
22S CYS* 1.3 60.0 + - - +
23S CYS* 4.2 4.0 - - - -
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Residues in contact with CYS 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D TRP* 3.5 28.3 - - + -
78F TYR* 3.6 0.9 - - - -
7S CYS* 3.2 1.0 - - - -
8S ILE* 2.9 34.0 + - + +
10S CYS* 4.2 3.8 - - - -
12S GLY 3.9 0.4 - - - -
13S CYS* 3.7 11.4 - - + -
14S CYS* 2.1 54.3 - - - -
15S HIS* 3.7 12.8 - - - -
20S GLY 4.2 4.3 - - - -
21S MET* 1.3 73.9 - - - +
23S CYS* 1.3 62.1 + - - +
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Residues in contact with CYS 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D TRP* 3.5 8.2 - - - -
78F TYR* 3.1 59.4 + - + -
80F PHE* 5.4 1.8 - - + -
5S PRO* 4.8 7.6 - - + -
6S ILE 3.4 4.0 - - - +
7S CYS* 2.0 46.0 - - - -
21S MET* 5.1 4.0 - - - -
22S CYS* 1.3 73.0 - - - +
24S LYS* 1.3 69.2 + - - +
25S THR* 3.3 5.4 + - - -
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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