Contacts of the strand formed by residues 23 - 28 (chain A) in PDB entry 1QM7
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 CYS 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A THR* 3.9 9.2 - - - -
2A MET 3.6 8.3 - - - -
3A CYS* 2.0 52.9 - - - -
22A ASN* 1.3 74.2 - - - +
24A TYR* 1.3 59.2 + - - +
39A GLY 3.4 3.4 - - - -
41A GLY 3.4 4.3 - - - -
53A CYS* 3.3 5.9 - - - +
54A CYS* 2.7 30.0 + - - -
56A THR 4.2 1.1 - - - -
59A CYS* 3.8 20.4 - - - -
60A ASN* 3.5 24.9 - - + +
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Residues in contact with TYR 24 (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 HIS 5.1 1.6 + - - -
23A CYS* 1.3 74.0 - - - +
25A LYS* 1.3 63.1 - - - +
26A LYS* 3.8 41.5 + - + -
37A GLY* 4.0 0.6 - - - -
38A ARG* 3.2 21.1 + - - +
39A GLY* 2.8 60.0 + - - -
40A CYS 3.4 11.7 - - - -
41A GLY 3.5 12.8 + - - +
43A PRO* 3.3 35.8 - - + +
51A LEU* 3.9 8.3 - - + -
52A ASN 3.2 9.9 - - - +
53A CYS* 4.1 2.2 - - - -
60A ASN* 3.0 21.0 - - - +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 1.3 77.9 - - - +
26A LYS* 1.3 58.8 + - - +
27A SER* 4.4 8.7 + - - +
35A VAL* 3.6 41.5 - - + -
37A GLY 3.6 3.6 - - - -
38A ARG* 3.8 2.9 - - + +
50A LYS 3.7 1.4 - - - +
51A LEU* 3.5 3.3 - - - +
52A ASN* 2.8 49.6 + - + +
60A ASN* 4.1 20.4 - - + +
61A TYR* 2.9 35.3 + - - -
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Residues in contact with LYS 26 (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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24A TYR* 3.8 32.9 + - + +
25A LYS* 1.3 74.1 - - - +
27A SER* 1.3 60.1 + - - +
35A VAL* 3.5 4.7 - - - +
36A LEU* 2.8 32.0 + - + -
37A GLY* 2.9 23.4 + - - +
43A PRO* 4.9 8.3 - - + -
44A THR 5.6 0.9 - - - -
45A VAL* 3.9 27.4 - - + -
49A ILE* 3.8 16.3 - - + +
50A LYS 3.5 4.3 - - - -
51A LEU* 4.6 3.4 - - + +
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Residues in contact with SER 27 (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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25A LYS* 4.4 9.2 - - - +
26A LYS* 1.3 77.1 + - - +
28A ARG* 1.3 67.3 + - - +
33A LYS* 5.7 2.7 - - - -
34A MET 3.3 10.8 - - - -
35A VAL* 3.8 18.7 - - - +
36A LEU* 4.1 6.7 - - - +
49A ILE* 3.3 8.3 - - - +
50A LYS* 2.8 45.0 + - - -
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Residues in contact with ARG 28 (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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27A SER* 1.3 74.4 - - - +
29A ARG* 1.3 64.3 + - - +
30A HIS* 2.7 15.3 + - - +
31A PRO 2.2 37.2 + - - -
32A PRO* 2.2 51.7 + - - +
33A LYS* 3.4 21.5 - - - +
34A MET* 2.8 34.0 + - - +
36A LEU* 3.8 25.0 - - + +
48A GLY 3.9 5.4 - - - +
50A LYS* 4.9 0.9 - - - +
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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