Contacts of the helix formed by residues 31 - 42 (chain B) in PDB entry 6YOV
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 THR 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 5.4 7.4 - - + +
67A PRO* 6.3 0.4 - - + -
28B GLN 4.8 4.3 - - - +
29B GLY 3.4 13.0 + - - +
30B ILE* 1.3 77.5 - - - +
32B LYS* 1.3 64.6 + - - +
33B PRO* 3.8 7.3 - - - -
34B ALA* 3.0 31.4 + - - +
35B ILE* 3.1 14.0 + - - +
56B ARG* 4.8 1.8 - - - +
61I A 3.2 48.4 + - - +
62I C 4.3 8.7 - - - +
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR* 1.3 72.3 - - - +
33B PRO* 1.3 62.5 - - + +
35B ILE 3.1 2.1 + - - -
36B ARG* 2.8 37.2 + - - +
49B GLY* 5.6 3.4 + - - -
52B TYR* 3.5 61.8 - - + +
56B ARG* 4.9 8.6 - - - +
62I C 4.5 7.7 + - - +
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Residues in contact with PRO 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR* 3.6 6.1 - - - +
32B LYS* 1.3 93.2 - - + +
34B ALA* 1.3 59.0 + - - +
36B ARG* 3.1 14.7 + - + +
37B ARG* 2.7 58.6 + - + +
61I A 3.4 32.1 - - + +
62I C 4.1 7.2 - - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.0 10.7 - - - +
63A ILE* 4.2 13.4 - - + +
64A ARG* 5.1 2.9 - - + +
30B ILE* 4.0 12.1 - - + -
31B THR* 3.0 33.0 + - - +
33B PRO* 1.3 77.5 - - - +
35B ILE* 1.3 63.2 + - - +
37B ARG* 3.5 18.7 + - - +
38B LEU* 3.3 27.7 + - - +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 6.3 0.9 - - + -
105A PHE* 4.1 9.2 - - + -
30B ILE* 3.8 18.6 - - + +
31B THR 3.1 13.1 + - - +
32B LYS 3.6 6.1 - - - +
34B ALA* 1.3 73.6 - - - +
36B ARG* 1.3 67.5 + - - +
38B LEU* 3.2 11.4 + - + +
39B ALA* 2.9 21.3 + - + +
47B ILE* 6.0 1.3 - - + -
51B ILE* 4.8 4.3 - - + -
52B TYR* 3.8 47.8 - - + +
55B THR* 4.0 33.4 - - + +
56B ARG* 4.1 22.4 - - + +
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS* 2.8 18.1 + - - +
33B PRO* 3.4 13.5 - - + +
35B ILE* 1.3 78.8 - - - +
37B ARG* 1.3 59.9 + - + +
39B ALA* 3.2 8.1 + - - +
40B ARG* 2.8 64.9 + - + +
47B ILE* 3.5 28.5 - - + +
52B TYR* 2.8 28.6 + - - +
83J G 3.5 27.3 + - - -
84J T 6.2 1.6 - - - +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.3 48.5 + - + +
62A LEU* 3.0 52.4 + - + +
64A ARG* 3.8 13.4 - - - +
33B PRO* 2.7 35.5 + - + +
34B ALA* 3.5 15.6 - - - +
36B ARG* 1.3 75.1 - - + +
38B LEU* 1.3 63.8 + - - +
40B ARG* 3.2 2.9 + - - +
41B ARG* 3.0 18.9 + - - +
60I A 4.7 2.2 + - - -
61I A 2.8 41.2 + - - -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.8 18.6 - - + -
63A ILE* 3.9 18.6 - - + -
98A GLU* 3.8 30.5 - - + +
101A LEU* 3.7 29.8 - - + -
102A VAL* 3.7 30.3 - - + +
105A PHE* 4.1 13.2 - - + -
30B ILE* 5.9 0.4 - - + -
34B ALA 3.3 16.5 + - - +
35B ILE* 3.2 11.3 + - + +
37B ARG* 1.3 76.6 - - - +
39B ALA* 1.3 63.9 + - - +
41B ARG* 3.2 6.3 + - - +
42B GLY* 3.2 17.0 + - - -
55B THR* 6.1 0.2 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.6 36.5 - - + -
35B ILE* 2.9 14.5 + - + +
36B ARG* 3.5 10.8 - - - +
38B LEU* 1.3 77.3 - - - +
40B ARG* 1.3 60.3 + - - +
42B GLY* 3.0 9.4 + - - -
43B GLY 3.2 0.5 + - - -
44B VAL* 2.9 41.9 + - + +
47B ILE* 4.5 9.2 - - + -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.9 3.2 - - - +
48A ALA* 3.6 22.4 - - - +
51A GLU* 3.3 35.6 - - + +
52A ILE* 3.4 33.3 - - - +
55A TYR* 3.7 15.5 - - + -
36B ARG* 2.8 56.7 + - + +
37B ARG* 3.5 6.7 - - - +
39B ALA* 1.3 73.5 - - - +
41B ARG* 1.3 65.8 + - - +
43B GLY 2.8 12.0 + - - -
44B VAL 3.0 21.9 + - - +
45B LYS 3.0 21.0 + - - -
47B ILE* 4.6 2.7 - - + +
83J G 4.5 4.4 + - - -
84J T 4.7 9.1 + - - -
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE 4.5 0.2 - - - -
55A TYR* 2.6 27.4 + - + +
56A GLN* 3.1 32.4 + - - +
58A SER* 2.8 39.2 + - - -
59A THR* 4.2 3.6 + - - +
60A GLU 3.3 24.9 + - - -
62A LEU* 3.7 25.7 - - + +
98A GLU* 4.2 10.3 + - - +
102A VAL* 3.9 24.6 - - + +
37B ARG 3.0 12.5 + - - +
38B LEU* 3.2 10.0 + - - +
40B ARG* 1.3 75.4 - - - +
42B GLY* 1.3 57.4 + - - +
107G GLY* 5.3 4.7 - - - -
108G VAL* 3.6 31.9 - - + +
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 4.6 2.0 - - - -
102A VAL* 4.0 25.3 - - - +
105A PHE* 4.6 0.9 - - - -
106A GLU* 3.5 34.0 - - - +
109A ASN* 4.3 5.5 + - - +
38B LEU 3.2 7.7 + - - -
39B ALA 3.0 10.6 + - - -
41B ARG* 1.3 76.5 - - - +
43B GLY* 1.3 56.6 + - - +
44B VAL* 3.6 2.0 - - - -
113G GLN* 5.4 1.9 + - - -
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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