Contacts of the strand formed by residues 35 - 44 (chain H) in PDB entry 2C2V
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 ASN 35 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H ASP* 3.2 21.2 + - - +
33H GLU 2.9 10.1 + - - -
34H SER* 1.3 71.9 - - - +
36H ALA* 1.4 60.2 + - - +
37H ARG* 4.1 10.6 + - - +
38H TYR* 2.8 45.9 + - + +
37I LYS* 3.2 62.5 + - - +
39I PRO* 3.7 19.2 - - - +
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Residues in contact with ALA 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ALA* 3.9 27.4 - - + -
8H LEU* 4.6 16.2 - - + -
12H ILE* 5.0 5.9 - - - +
16H THR* 5.2 2.8 + - - +
31H PRO* 4.1 12.4 - - - +
32H ASP 4.2 5.6 - - - -
34H SER* 4.1 3.6 - - - +
35H ASN* 1.4 75.9 + - - +
37H ARG* 1.4 55.1 + - - +
38H TYR 3.2 3.9 + - - -
39H PHE* 3.6 16.3 - - - -
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Residues in contact with ARG 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 4.2 14.0 - - + +
9H PRO* 3.3 34.6 - - - +
12H ILE* 3.9 19.1 - - + +
35H ASN* 4.1 8.9 + - - +
36H ALA* 1.4 75.1 - - + +
38H TYR* 1.3 57.0 + - - -
39H PHE* 3.8 10.3 - - - -
61H PHE* 3.3 17.2 - - + -
62H LEU* 3.3 54.7 + - + +
63H PRO 3.4 17.6 + - - -
64H GLU* 3.9 8.7 + - - +
66H TYR* 5.0 1.4 + - - +
36I VAL* 3.5 41.7 - - - +
37I LYS 5.2 0.9 - - - +
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Residues in contact with TYR 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H PRO* 3.0 6.6 - - - +
32H ASP* 3.0 53.6 + - + -
35H ASN* 2.8 36.6 + - + +
36H ALA 3.2 1.6 + - - -
37H ARG* 1.3 74.0 - - - +
39H PHE* 1.3 65.6 + - - +
40H HIS* 3.3 28.6 + + - -
59H GLU* 2.0 47.4 + - + +
60H LEU 3.7 7.9 - - - -
61H PHE* 4.2 3.8 - - + -
76H MET* 4.6 4.7 - - - +
37I LYS* 6.0 0.4 - - - -
39I PRO* 3.6 32.8 - - + -
41I ASN* 4.3 5.8 + - + -
42I PHE* 4.1 5.2 - + - -
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Residues in contact with PHE 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 5.3 2.5 - - + -
16H THR* 3.9 34.8 - - + -
19H LEU* 5.8 6.3 - - + -
29H ALA* 4.9 9.2 - - + -
30H GLU* 3.3 21.5 - - - +
31H PRO* 4.3 5.2 - - + -
36H ALA 3.6 21.1 - - - -
37H ARG 3.8 10.3 - - - -
38H TYR* 1.3 85.7 - - - +
40H HIS* 1.3 61.3 + - - +
41H VAL* 3.3 14.3 - - + +
59H GLU* 3.4 5.4 - - - +
60H LEU* 2.7 60.3 + - + +
62H LEU* 4.3 16.8 - - + -
105H ILE* 4.7 20.2 - - + -
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Residues in contact with HIS 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LYS* 3.7 1.6 - - - +
29H ALA 3.6 0.9 - - - -
30H GLU* 2.9 31.1 + - + +
31H PRO 3.7 11.9 - - - -
32H ASP* 2.7 41.6 + - + +
38H TYR* 3.3 35.1 + + - -
39H PHE* 1.3 68.8 - - - +
41H VAL* 1.3 59.6 + - - +
42H VAL* 5.3 1.1 - - + -
58H LEU 4.0 3.8 - - - -
59H GLU* 4.9 3.6 - - - +
76H MET* 6.3 1.0 - - - +
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 4.6 4.9 - - + -
28H LYS 2.6 20.9 - - - +
29H ALA* 4.7 6.3 - - + -
39H PHE* 3.3 25.8 - - + +
40H HIS* 1.3 75.9 - - - +
42H VAL* 1.4 71.7 + - - +
43H ILE* 3.7 24.9 - - + -
56H PHE 3.3 0.2 - - - +
57H LYS* 3.6 1.6 - - - +
58H LEU* 2.7 49.6 + - + +
59H GLU 4.7 0.2 - - - -
60H LEU* 4.3 14.4 - - + +
109H LEU* 4.1 19.1 - - + -
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Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY 3.7 1.4 - - - +
27H ILE* 3.7 1.7 - - - -
28H LYS* 2.8 45.2 + - + +
40H HIS 5.3 0.7 - - - -
41H VAL* 1.4 87.2 - - - +
43H ILE* 1.3 71.3 + - - +
44H ALA 3.2 3.1 + - - -
55H THR* 4.4 14.6 - - + -
56H PHE 3.2 19.7 - - - +
57H LYS* 4.9 9.9 - - + +
156H ILE* 6.1 0.7 - - - +
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Residues in contact with ILE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 3.1 34.5 - - + -
41H VAL* 3.7 23.1 - - + -
42H VAL* 1.3 76.1 - - - +
44H ALA* 1.3 84.4 + - - +
45H GLY 3.2 2.6 + - - -
55H THR* 3.5 4.0 - - - -
56H PHE* 2.9 39.8 + - + +
58H LEU* 3.7 15.7 - - + -
75H PHE* 6.0 1.1 - - + -
109H LEU* 4.7 8.7 - - + +
112H ILE* 4.7 17.5 - - + -
113H GLN* 4.2 15.0 - - + +
116H LEU* 4.0 19.1 - - + -
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Residues in contact with ALA 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY* 3.1 36.8 + - - +
42H VAL 3.2 0.2 + - - -
43H ILE* 1.3 90.5 - - + +
45H GLY* 1.4 71.3 + - - +
46H PRO* 2.8 15.6 - - - +
54H GLY 4.8 2.2 - - - -
55H THR* 4.9 6.7 - - + -
56H PHE* 5.0 0.7 - - - -
113H GLN* 5.1 1.8 - - - +
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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