Contacts of the strand formed by residues 19 - 27 (chain A) in PDB entry 3QN3
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 PRO 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 GLU* 3.9 23.6 - - + +
12A VAL 3.2 9.6 - - - +
13A LEU* 4.3 2.2 - - + -
14A ASP* 4.7 0.9 - - - +
18A ASN* 1.3 92.2 - - + +
20A THR* 1.3 62.0 + - - +
52A ARG* 2.9 25.9 + - - -
58A PHE* 3.3 51.8 - - + -
61A LYS* 3.4 28.9 - - + +
62A GLY* 4.1 0.4 - - - -
63A VAL* 4.1 2.9 - - + -
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Residues in contact with THR 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 GLU* 3.6 0.9 - - - -
12A VAL* 2.9 37.0 + - + -
14A ASP* 4.0 27.8 - - + +
19A PRO* 1.3 75.8 - - - +
21A VAL* 1.3 65.2 + - - +
36A ILE* 3.6 19.7 - - + -
37A VAL* 2.6 35.7 + - - +
38A PRO 4.3 5.7 + - - -
39A SER* 5.0 1.6 - - - -
50A GLU* 5.5 1.0 + - - -
52A ARG* 5.1 4.2 + - - +
63A VAL* 3.4 21.1 - - - +
108A ASN* 5.1 4.0 + - - +
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.9 18.2 - - + -
10A TYR 3.9 2.7 - - - -
12A VAL* 4.3 1.6 - - - -
20A THR* 1.3 80.5 + - - +
22A LYS* 1.3 74.1 + - - +
23A ALA* 4.1 5.4 - - + +
36A ILE* 3.5 3.6 - - - +
37A VAL* 3.0 31.4 + - + +
63A VAL* 3.8 17.5 - - + -
66A ALA* 3.7 29.4 - - + -
67A VAL* 4.2 7.2 - - + -
70A VAL* 4.7 8.7 - - + -
108A ASN* 3.8 31.6 - - + +
109A ALA 5.6 0.4 - - - +
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Residues in contact with LYS 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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9A ALA* 3.1 3.8 - - - +
10A TYR* 2.9 62.2 + - + +
12A VAL* 3.7 25.8 - - + +
20A THR 3.9 1.0 + - - -
21A VAL* 1.3 75.3 - - - +
23A ALA* 1.3 65.6 + - - +
34A ALA* 3.8 23.6 - - + +
35A ALA 3.3 11.4 - - - +
36A ILE* 3.7 26.9 - - + +
366A GLU* 5.3 3.0 + - - +
397B ASN* 6.0 2.7 - - + +
401B GLU* 2.6 26.8 + - - +
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Residues in contact with ALA 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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7A VAL* 6.0 0.2 - - + -
8A ARG 3.3 10.1 - - - +
9A ALA* 4.1 6.5 - - + +
21A VAL* 4.1 4.2 - - + -
22A LYS* 1.3 75.1 - - - +
24A GLU* 1.3 61.9 + - - +
25A VAL* 5.6 0.4 - - + -
34A ALA* 3.2 6.2 - - - +
35A ALA 2.9 30.5 + - - -
70A VAL* 5.3 0.4 - - + -
109A ALA 5.5 0.2 - - - +
112A GLY* 3.5 37.0 - - - +
113A VAL* 3.9 15.0 - - + +
116A ALA* 3.8 2.9 - - + +
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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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6A ASP* 4.0 4.0 - - - +
7A VAL* 3.5 2.4 - - - -
8A ARG* 2.8 84.0 + - + +
10A TYR* 4.8 13.5 + - + +
23A ALA* 1.3 76.6 - - - +
25A VAL* 1.3 65.3 + - - +
26A THR* 4.1 9.9 + - - -
32A VAL* 3.5 27.5 - - + +
33A GLY 3.3 6.1 - - - +
34A ALA* 4.4 8.3 - - + -
116A ALA* 4.3 0.2 - - - -
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Residues in contact with VAL 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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4A ILE* 3.9 19.3 - - + -
6A ASP 3.3 8.1 - - - +
7A VAL* 4.3 18.4 - - + -
24A GLU* 1.3 79.0 - - - +
26A THR* 1.3 64.2 + - - +
27A LEU* 4.0 17.7 - - + -
32A VAL* 3.4 3.7 - - - +
33A GLY 2.8 34.0 + - - +
113A VAL* 4.2 7.9 - - + +
116A ALA* 3.7 27.8 - - + +
117A THR* 3.7 26.5 - - - +
120A ALA* 3.6 3.7 - - + +
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Residues in contact with THR 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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4A ILE* 3.9 0.7 - - - -
5A GLU* 2.8 30.1 + - + +
6A ASP* 2.8 32.7 + - + +
24A GLU* 4.1 13.2 + - - -
25A VAL* 1.3 75.7 - - - +
27A LEU* 1.3 76.6 + - - +
30A GLY* 4.3 9.4 - - - +
31A SER 3.4 9.0 - - - +
32A VAL* 3.6 20.3 - - + +
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Residues in contact with LEU 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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2A LEU* 4.0 18.4 - - + -
3A VAL 3.3 10.5 - - - +
4A ILE* 4.1 8.3 - - + -
5A GLU* 3.7 7.8 - - - +
25A VAL* 4.0 19.1 - - + -
26A THR* 1.3 85.5 - - - +
28A SER* 1.3 58.2 + - - +
29A ASP* 3.2 14.4 - - - +
30A GLY* 2.9 21.4 + - - -
31A SER* 2.9 11.0 + - - +
83A ALA* 3.7 31.4 - - + -
84A PHE* 5.4 0.2 - - + -
117A THR* 5.1 3.4 - - + -
120A ALA* 3.4 41.1 - - + +
121A ALA* 3.7 7.4 - - - +
124A ALA* 4.1 2.5 - - + -
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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