Contacts of the strand formed by residues 19 - 27 (chain A) in PDB entry 3QQN
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 VAL 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN* 3.2 38.4 - - + +
13A ARG* 4.1 14.8 - - + +
18A SER* 1.3 77.6 - - - +
20A GLU* 1.3 73.1 + - - +
21A LEU* 4.4 11.4 - - + -
72A ILE 4.1 0.6 - - - +
73A SER* 3.4 3.5 - - - -
74A ILE* 3.0 48.0 + - + +
77A LEU* 4.0 18.6 - - + +
85A TYR* 6.0 0.2 - - + -
113A VAL* 4.5 19.3 - - + -
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Residues in contact with GLU 20 (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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11A GLN* 4.1 12.6 + - - +
19A VAL* 1.3 79.6 - - - +
21A LEU* 1.3 72.6 + - - +
22A HIS* 6.0 1.6 - - + -
71A THR* 3.7 26.8 - - + +
72A ILE 3.4 4.7 - - - -
73A SER* 3.9 13.4 + - - +
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Residues in contact with LEU 21 (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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8A PRO* 4.3 2.0 - - + -
9A LEU 3.4 33.0 - - - +
11A GLN* 4.0 9.9 - - - +
19A VAL* 4.4 8.3 - - + -
20A GLU* 1.3 82.6 - - - +
22A HIS* 1.3 61.3 + - - +
35A TRP* 3.8 13.8 - - + -
71A THR* 3.4 7.0 - - - +
72A ILE* 2.9 47.8 + - + +
74A ILE* 6.2 1.1 - - + -
85A TYR* 3.5 42.0 - - + -
111A ALA* 4.4 7.2 - - + -
113A VAL* 4.0 20.9 - - + -
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Residues in contact with HIS 22 (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 GLN* 3.3 28.0 - - - +
7A ALA 3.5 4.9 - - - +
8A PRO* 3.1 27.7 - - - +
9A LEU 5.3 0.4 - - - +
20A GLU* 6.0 1.8 - - + -
21A LEU* 1.3 76.4 - - - +
23A CYS* 1.3 67.0 + - - +
24A GLU* 2.7 32.7 + - + +
35A TRP* 4.0 1.6 - - - -
69A ALA* 4.3 5.6 - - + -
70A SER 3.3 21.5 + - - -
71A THR* 2.6 29.4 + - + +
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Residues in contact with CYS 23 (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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4A PHE* 3.5 19.3 - - - -
6A GLN 3.4 7.4 - - - +
8A PRO* 4.5 4.0 - - + -
22A HIS* 1.3 78.1 + - - +
24A GLU* 1.3 70.0 + - - +
33A ILE* 3.9 10.0 - - + +
35A TRP* 3.6 15.5 - - + -
69A ALA* 3.6 0.5 - - - -
70A SER 2.9 31.7 + - - +
87A CYS* 2.0 50.7 - - + -
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Residues in contact with GLU 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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4A PHE* 3.5 6.8 - - - -
5A VAL* 3.0 35.6 + - + +
6A GLN* 2.9 29.9 + - + +
22A HIS* 2.7 30.5 + - + +
23A CYS* 1.3 81.6 - - - +
25A ALA* 1.3 63.5 + - - +
33A ILE* 4.5 0.4 - - - -
67A HIS* 3.2 29.2 + - + -
68A ALA 3.2 6.7 - - - +
69A ALA* 3.9 8.3 - - - +
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Residues in contact with ALA 25 (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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3A GLY 3.2 16.2 - - - +
4A PHE* 4.3 4.9 - - + -
5A VAL* 4.2 2.2 - - - +
24A GLU* 1.3 77.1 - - - +
26A VAL* 1.3 68.7 + - - +
31A PRO* 4.2 10.0 - - + +
33A ILE* 4.5 3.6 - - + -
67A HIS* 3.8 1.2 - - - +
68A ALA* 2.8 39.6 + - + +
89A ALA* 3.9 28.7 - - + -
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Residues in contact with VAL 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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2A ALA* 3.3 5.0 - - - -
3A GLY 2.9 39.3 + - - +
5A VAL* 4.2 28.9 - - + -
25A ALA* 1.3 80.1 - - - +
27A GLY* 1.3 59.3 + - - +
31A PRO* 3.6 9.0 - - - +
66A GLN 5.3 2.2 - - - +
67A HIS* 4.0 20.4 - - + +
9B LEU* 4.4 12.8 - - + -
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Residues in contact with GLY 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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1A MSE 3.3 16.4 - - - -
26A VAL* 1.3 79.3 - - - +
28A SER* 1.3 62.3 + - - -
29A PRO 3.0 16.4 - - - +
30A VAL* 3.6 10.4 + - - +
31A PRO* 3.6 4.9 - - - +
66A GLN 4.8 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