Contacts of the strand formed by residues 34 - 47 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLN* 3.6 24.7 - - + -
16C ALA* 3.6 13.7 - - + -
17C LYS* 3.5 61.8 - - + +
20C VAL* 3.9 21.4 - - + +
33C THR* 1.3 79.8 - - - +
35C ASN* 1.3 72.2 + - - +
36C LYS* 3.4 25.6 - - - -
64C VAL* 3.9 13.9 - - + -
65C TYR 4.0 2.9 - - - -
66C ALA* 4.2 1.6 - - - -
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Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C THR* 3.5 13.3 + - - +
34C PHE* 1.3 89.6 + - - +
36C LYS* 1.3 70.1 + - + +
65C TYR* 2.8 24.8 + - + +
66C ALA 3.1 8.7 + - - -
67C SER* 3.1 11.4 + - - +
68C ASP* 2.8 40.6 + - - +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLN* 3.5 8.7 - - - +
34C PHE* 3.4 17.6 - - + -
35C ASN* 1.3 84.5 - - + +
37C ALA* 1.3 66.6 + - - +
38C ILE* 3.6 22.6 + - + -
64C VAL* 3.4 0.4 - - - +
65C TYR* 2.6 55.2 + - + +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.3 6.8 - - + +
12C THR* 4.5 17.5 - - + +
13C GLN* 2.8 34.8 + - - +
16C ALA* 3.5 25.1 - - + -
34C PHE* 4.2 0.4 - - - -
36C LYS* 1.3 77.3 - - - +
38C ILE* 1.3 64.0 + - - +
41C CYS* 4.8 3.1 - - - -
62C LEU* 5.1 2.0 - - + -
63C TYR 3.2 15.5 - - - +
64C VAL* 4.0 0.7 - - - +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.7 11.0 - - + -
36C LYS* 3.6 29.4 - - - -
37C ALA* 1.3 78.8 - - - +
39C ARG* 1.3 72.7 + - - +
41C CYS* 3.3 19.4 - - - -
63C TYR* 3.1 22.3 + - + +
65C TYR* 4.0 25.8 - - + +
70C LEU* 4.1 11.4 - - + -
95C PRO* 5.5 0.9 - - + -
96C PRO* 3.9 23.6 - - + -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.9 11.3 - - - +
6C ILE 4.4 5.2 + - - +
7C ASP* 2.4 43.7 + - - +
8C ILE* 3.6 30.2 - - + +
38C ILE* 1.3 84.5 - - - +
40C PRO* 1.4 70.6 - - + +
41C CYS 4.1 0.7 - - - +
63C TYR* 4.9 0.4 - - - -
96C PRO* 3.6 13.5 - - - +
1D GLY 5.5 5.2 - - - -
3D TRP* 4.5 14.3 + - + +
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Residues in contact with PRO 40 (chain C).
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* 5.0 7.2 - - + -
39C ARG* 1.4 85.8 - - + +
41C CYS* 1.3 63.0 + - - +
42C MET* 5.3 1.7 - - - +
61C GLN 4.4 2.4 - - - +
63C TYR* 3.3 29.0 - - + -
96C PRO* 3.5 20.9 - - + -
3D TRP* 3.4 53.6 - - + +
42D MET* 4.3 20.8 - - - +
61D GLN* 4.7 2.2 - - - +
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Residues in contact with CYS 41 (chain C).
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* 3.5 6.9 - - - +
6C ILE* 2.9 51.6 + - + +
8C ILE* 3.9 13.9 - - + -
12C THR* 4.0 19.1 - - + -
37C ALA* 4.8 1.6 - - - -
38C ILE 3.3 23.3 - - - -
39C ARG* 4.1 2.0 - - - +
40C PRO* 1.3 75.0 - - - +
42C MET* 1.3 63.0 + - - +
61C GLN 3.6 4.5 - - - +
62C LEU* 3.9 24.2 - - + -
63C TYR 3.9 3.6 - - - -
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Residues in contact with MET 42 (chain C).
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* 3.5 17.0 - - + -
4C GLU 3.4 6.5 - - - +
5C ILE* 4.4 2.7 - - + -
6C ILE* 4.7 3.7 - - - +
40C PRO 5.3 0.9 - - - +
41C CYS* 1.3 80.3 - - - +
43C LYS* 1.3 60.5 + - - +
60C TYR* 3.4 7.6 - - - +
61C GLN* 3.0 72.9 + - + +
62C LEU* 4.7 0.9 - - - +
5D ILE* 3.9 18.6 - - + -
40D PRO* 3.8 29.4 - - + -
42D MET* 3.3 40.2 - - + +
63D TYR* 5.5 0.9 - - + -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLU 3.8 1.2 - - - +
3C TRP* 3.5 4.7 - - - -
4C GLU* 2.9 38.3 + - + +
6C ILE* 3.8 25.4 - - + -
11C PHE* 5.3 4.0 - - - -
42C MET* 1.3 75.3 - - - +
44C LYS* 1.3 68.0 + - - +
45C THR* 4.1 4.3 + - - +
58C TYR* 3.4 36.9 - - + -
59C GLU 3.2 5.6 - - - +
60C TYR* 3.2 46.4 + - + -
77C GLU* 5.0 0.4 + - - -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLY 3.6 28.0 - - - +
2C GLU 3.4 4.9 - - - +
3C TRP* 3.4 43.6 - - + +
43C LYS* 1.3 73.7 - - - +
45C THR* 1.3 65.2 + - - +
46C ILE* 3.5 27.1 + - + +
58C TYR* 3.2 6.1 - - - +
59C GLU* 2.7 65.6 + - + +
96D PRO 3.7 14.4 + - - -
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLY* 3.1 28.4 + - - -
2C GLU 3.4 9.2 + - - -
43C LYS* 4.1 5.7 + - - +
44C LYS* 1.3 73.3 - - - +
46C ILE* 1.3 63.4 + - - +
47C TYR* 3.7 35.8 - - + +
55C ILE* 4.3 19.3 - - + -
57C GLY 3.9 3.1 - - - -
58C TYR* 3.3 22.8 - - + -
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLY 4.8 4.0 - - - +
44C LYS* 3.5 34.8 - - + +
45C THR* 1.3 74.0 - - - +
47C TYR* 1.3 66.9 + - - +
55C ILE* 3.5 3.1 - - - +
56C LYS* 2.6 48.8 + - + -
57C GLY* 2.9 24.2 + - - +
58C TYR 4.7 4.0 - - - +
59C GLU* 4.2 24.7 - - + +
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Residues in contact with TYR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLY* 4.7 13.9 - - - +
2C GLU 5.6 1.3 - - - -
45C THR* 3.7 30.2 - - + +
46C ILE* 1.3 85.4 - - - +
48C GLU* 1.3 68.1 + - - +
49C ASN* 5.4 1.6 + - - -
51C GLY 5.5 1.6 - - - +
53C ARG* 4.0 37.6 - - + -
54C GLU 3.1 17.7 - - - +
55C ILE* 3.8 20.9 - - + +
56C LYS* 4.1 3.9 - - - +
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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