Contacts of the strand formed by residues 34 - 47 (chain D) in PDB entry 3Q2P
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 PHE 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLN* 3.7 38.4 - - + -
16D ALA* 3.7 13.5 - - + -
17D LYS* 3.6 45.8 - - + -
20D VAL* 3.8 36.0 - - + +
21D ASP* 5.8 1.1 - - - +
32D LEU 3.9 3.0 + - - -
33D THR* 1.3 81.4 - - - +
35D ASN* 1.3 84.4 + - - +
36D LYS* 3.8 5.6 - - - -
37D ALA 4.2 0.2 - - - -
64D VAL* 3.9 8.5 - - + -
65D TYR 4.3 1.3 - - - -
66D ALA* 4.4 0.9 - - - -
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Residues in contact with ASN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 3.2 9.6 + - - +
34D PHE* 1.3 94.6 + - - +
36D LYS* 1.3 67.6 + - + +
65D TYR* 2.8 24.5 + - + +
66D ALA* 2.9 6.6 + - - -
67D SER* 2.7 29.2 + - - +
68D ASP* 2.9 28.2 + - - +
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Residues in contact with LYS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 6.3 0.9 - - + -
13D GLN* 3.6 14.1 - - - +
34D PHE* 3.8 8.5 - - - -
35D ASN* 1.3 84.3 - - + +
37D ALA* 1.3 68.3 + - - +
38D ILE* 3.8 21.5 + - + +
64D VAL* 4.3 0.7 - - - -
65D TYR* 2.7 46.1 + - + +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.9 8.0 - - + +
12D THR* 4.2 19.5 - - + +
13D GLN* 2.8 35.0 + - - +
16D ALA* 3.7 22.4 - - + -
34D PHE* 4.2 2.8 - - - -
36D LYS* 1.3 79.5 - - - +
38D ILE* 1.3 63.9 + - - +
41D CYS* 4.6 5.6 - - - -
62D LEU* 5.0 1.3 - - + -
63D TYR 3.3 11.0 - - - +
64D VAL* 4.3 2.0 - - - +
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.7 12.1 - - + -
36D LYS* 3.8 26.5 - - + +
37D ALA* 1.3 78.7 - - - +
39D ARG* 1.3 74.5 + - - +
40D PRO 3.8 1.0 - - - +
41D CYS* 3.0 23.4 - - - -
63D TYR* 3.0 29.5 + - + +
65D TYR* 3.9 26.5 - - + +
70D LEU* 4.1 16.8 - - + -
95D PRO* 6.0 0.2 - - + -
96D PRO* 4.1 15.5 - - + -
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TRP* 4.8 8.9 + - + -
5D ILE* 5.6 5.8 - - + +
6D ILE 4.7 4.5 + - - +
7D ASP* 4.1 30.1 - - - +
8D ILE* 4.0 34.8 - - + +
38D ILE* 1.3 84.5 - - - +
40D PRO* 1.3 68.1 - - + +
41D CYS 4.3 0.9 - - - +
63D TYR* 4.6 1.1 - - - -
96D PRO* 3.4 17.0 - - - +
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Residues in contact with PRO 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TRP* 3.6 41.5 - - + +
42C MET* 3.8 35.2 - - + -
5D ILE* 4.5 9.0 - - + -
39D ARG* 1.3 88.5 - - + +
41D CYS* 1.3 70.0 + - - +
42D MET* 5.3 2.9 - - + +
61D GLN 4.3 3.3 - - - +
63D TYR* 3.6 30.2 - - + -
96D PRO* 3.9 7.4 - - + -
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Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.5 5.9 - - - +
6D ILE* 3.0 47.0 + - + +
8D ILE* 3.9 12.7 - - + +
12D THR* 4.1 19.7 - - + -
37D ALA* 4.6 2.0 - - - -
38D ILE 3.0 28.7 - - - -
39D ARG* 4.3 0.6 - - - +
40D PRO* 1.3 77.1 - - - +
42D MET* 1.3 64.0 + - - +
61D GLN 3.5 5.8 - - - +
62D LEU* 3.9 26.9 - - + -
63D TYR 4.0 3.8 - - - -
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Residues in contact with MET 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.1 10.1 - - + -
40C PRO* 4.3 18.8 - - + -
42C MET* 3.3 44.4 - - + +
61C GLN* 4.9 4.9 - - - +
63C TYR* 5.8 1.1 - - + -
3D TRP* 3.7 14.8 - - + -
4D GLU 3.2 10.8 - - - +
5D ILE* 4.0 14.4 - - + -
6D ILE* 4.9 1.6 - - - +
40D PRO* 5.3 4.3 - - + +
41D CYS* 1.3 78.5 - - - +
43D LYS* 1.3 61.3 + - - +
60D TYR* 3.3 10.9 - - - +
61D GLN* 3.0 63.2 + - + +
62D LEU* 5.1 0.3 - - - +
63D TYR* 6.2 2.0 - - + -
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLU 3.4 1.4 - - - +
3D TRP* 3.3 5.5 - - - -
4D GLU* 2.8 71.7 + - + +
6D ILE* 4.0 16.6 - - + -
42D MET* 1.3 75.3 - - - +
44D LYS* 1.3 66.1 + - - +
45D THR* 4.0 2.0 + - - -
58D TYR* 3.5 36.3 + - + -
59D GLU 3.4 3.4 - - - +
60D TYR* 3.5 35.6 + - + -
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Residues in contact with LYS 44 (chain D).
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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96C PRO* 2.7 36.0 + - - -
1D GLY* 3.8 18.2 - - - -
2D GLU 3.2 17.9 - - - +
3D TRP* 3.2 41.6 - - + +
43D LYS* 1.3 73.5 - - - +
45D THR* 1.3 64.7 + - - +
46D ILE* 3.8 17.8 + - + +
58D TYR* 3.3 8.0 - - - +
59D GLU* 2.7 60.7 + - + +
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Residues in contact with THR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D GLY* 3.1 4.3 - - - -
2D GLU* 2.8 36.6 + - - -
4D GLU* 4.0 16.3 + - - -
43D LYS* 4.0 1.6 + - - -
44D LYS* 1.3 73.4 - - - +
46D ILE* 1.3 62.8 + - - +
47D TYR* 3.5 41.5 + - + +
55D ILE* 4.2 14.1 - - + -
57D GLY 4.1 2.0 - - - -
58D TYR* 3.8 28.4 - - + -
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D GLY* 4.4 6.3 - - - +
44D LYS* 3.9 24.5 - - + +
45D THR* 1.3 75.2 - - - +
47D TYR* 1.3 71.3 - - - +
55D ILE* 3.7 4.9 - - - +
56D LYS* 2.8 46.0 + - + -
57D GLY* 3.1 18.3 + - - +
58D TYR 4.5 11.4 - - - +
59D GLU* 4.3 26.7 - - + +
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Residues in contact with TYR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D GLY* 5.0 7.9 - - - +
2D GLU* 4.1 26.8 + - + -
45D THR* 3.5 37.6 + - + +
46D ILE* 1.3 85.6 - - - +
48D GLU* 1.3 66.0 + - - +
49D ASN* 3.9 18.8 - - - +
50D GLU* 6.2 0.2 - - - -
53D ARG* 3.3 61.4 + - + -
54D GLU 3.4 9.0 - - - +
55D ILE* 3.8 22.9 - - + +
56D LYS* 4.6 4.3 - - - +
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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