Contacts of the helix formed by residues 77 - 90 (chain B) in PDB entry 5U07
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 VAL 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.3 16.4 - - + -
55B VAL* 4.6 12.3 - - + -
76B ALA* 1.3 78.7 - - - +
78B GLU* 1.3 63.9 + - + +
80B ALA* 3.0 7.0 + - + +
81B PHE* 2.8 55.3 + - + -
196B ILE* 6.0 0.4 - - + -
200B ALA* 3.7 28.9 + - + +
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Residues in contact with GLU 78 (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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48B HIS* 4.9 2.8 - - - -
55B VAL* 3.2 27.1 - - + -
76B ALA 4.1 5.1 - - - +
77B VAL* 1.3 83.1 - - + +
79B ARG* 1.3 63.6 + - - +
81B PHE* 3.9 0.9 - - - +
82B TYR* 3.0 59.4 + - + -
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Residues in contact with ARG 79 (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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34B GLY 5.3 2.0 + - - -
35B VAL 6.1 4.2 - - - -
44B MET* 4.7 17.8 - - - +
76B ALA* 3.4 14.5 + - - +
77B VAL 3.3 0.6 - - - -
78B GLU* 1.3 77.9 - - - +
80B ALA* 1.3 64.7 + - - +
82B TYR* 4.2 5.8 - - - +
83B ALA* 3.0 50.2 + - - +
169B LEU* 4.2 16.3 + - + +
170B ASP* 4.7 15.4 + - - -
173B HIS* 3.4 49.4 + - + +
174B ARG* 6.1 0.6 - - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA 3.1 8.6 + - - +
77B VAL* 3.0 13.7 + - + +
79B ARG* 1.3 77.4 - - - +
81B PHE* 1.3 63.3 + - - +
83B ALA* 3.8 0.7 - - - +
84B VAL* 2.9 29.0 + - - +
173B HIS* 3.5 13.2 - - - -
196B ILE* 4.2 7.0 - - + +
199B LEU* 3.6 39.4 - - + +
200B ALA* 3.7 6.1 - - + +
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Residues in contact with PHE 81 (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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6B ILE* 4.1 15.5 - - + -
9B HIS* 4.2 11.9 - - + -
10B ALA* 3.6 29.8 - - - -
13B LEU* 3.3 26.2 - - + +
54B TYR* 4.5 10.1 - - + -
55B VAL* 3.5 35.2 - - + -
77B VAL* 2.8 49.1 + - + +
78B GLU 3.9 0.2 - - - +
80B ALA* 1.3 72.1 - - - +
82B TYR* 1.3 64.9 + - + +
84B VAL* 3.1 5.1 - - - +
85B ALA* 2.9 27.6 + - - +
196B ILE* 3.4 28.2 - - + +
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 5.8 0.2 - - - -
44B MET* 4.6 22.2 - - - -
47B ALA* 6.5 0.9 - - + -
48B HIS* 3.2 32.0 + + - -
51B VAL* 3.4 32.9 - - + +
52B ALA* 3.2 30.3 + - - +
55B VAL* 3.5 24.1 - - + +
78B GLU* 3.0 51.2 + - + +
79B ARG* 4.2 5.8 - - - +
81B PHE* 1.3 75.9 - - - +
83B ALA* 1.3 64.1 + - - +
85B ALA* 3.9 4.4 - - - +
86B ALA* 3.0 25.9 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 5.2 4.3 - - - +
35B VAL* 5.2 4.4 - - - +
44B MET* 6.4 0.2 - - - -
79B ARG* 3.0 29.7 + - - +
82B TYR* 1.3 78.4 - - - +
84B VAL* 1.3 57.2 + - - +
86B ALA* 3.3 5.3 + - - +
87B ILE* 2.9 33.6 + - - +
173B HIS* 3.0 35.4 - - + +
199B LEU* 5.3 0.4 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.7 0.2 - - + -
80B ALA 2.9 21.4 + - - +
81B PHE* 3.1 15.7 - - + +
83B ALA* 1.3 75.1 - - - +
85B ALA* 1.3 59.0 + - + +
87B ILE* 3.2 9.8 - - + +
88B MET* 2.8 33.6 + - + +
192B TRP* 4.4 16.2 - - + +
195B LEU* 3.5 27.6 - - + -
196B ILE* 3.3 42.2 - - + -
199B LEU* 4.4 6.4 - - + +
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Residues in contact with ALA 85 (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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13B LEU* 4.6 11.2 - - + -
17B VAL* 4.6 13.9 - - + -
31B LEU* 4.3 4.8 - - + +
51B VAL* 4.0 26.5 - - + -
81B PHE 2.9 17.7 + - - +
82B TYR 3.9 2.7 - - - +
84B VAL* 1.3 80.4 - - + +
86B ALA* 1.3 62.8 + - - +
88B MET* 3.6 9.9 - - - +
89B ALA* 2.9 24.5 + - - +
196B ILE* 6.2 0.7 - - + -
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Residues in contact with ALA 86 (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 LEU* 3.4 28.2 - - + +
32B ARG* 4.2 3.2 - - - -
34B GLY 3.8 24.0 - - - +
35B VAL* 4.2 4.7 - - - +
44B MET* 6.5 0.2 - - - -
47B ALA* 6.1 2.5 - - + -
82B TYR 3.0 18.5 + - - +
83B ALA 3.7 3.1 - - - +
85B ALA* 1.3 77.0 - - - +
87B ILE* 1.3 62.9 + - - +
89B ALA* 2.9 16.5 + - - +
90B ALA* 2.9 14.9 + - - +
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Residues in contact with ILE 87 (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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35B VAL* 3.7 23.0 - - + +
83B ALA 2.9 19.8 + - - +
84B VAL* 3.2 22.7 - - + +
86B ALA* 1.3 72.8 - - - +
88B MET* 1.3 67.7 + - - +
90B ALA* 3.1 12.1 + - + +
91B GLN* 3.4 18.4 - - - +
176B LEU* 3.8 13.2 - - + -
177B PRO* 3.3 39.7 - - + +
180B VAL* 3.3 21.1 - - + -
181B LEU* 4.9 7.4 - - + -
192B TRP* 6.1 0.9 - - + -
195B LEU* 5.7 2.7 - - + -
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Residues in contact with MET 88 (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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13B LEU 5.1 1.1 - - - +
14B VAL* 4.9 7.9 - - + +
17B VAL* 3.5 37.5 - - + -
18B SER* 4.2 17.7 - - - +
21B ILE* 4.3 10.7 - - + +
84B VAL* 2.8 21.9 + - + +
85B ALA* 3.6 6.1 - - - +
87B ILE* 1.3 79.4 - - - +
89B ALA* 1.3 61.3 + - - +
91B GLN* 3.5 18.7 - - - +
96B ARG* 6.0 1.2 - - - +
192B TRP* 3.3 60.8 - - + +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.4 33.0 - - + +
28B ARG* 4.6 4.0 - - - +
31B LEU* 3.4 33.2 - - + -
32B ARG* 4.1 10.0 + - - +
85B ALA 2.9 14.1 + - - +
86B ALA 2.9 10.1 + - - +
88B MET* 1.3 75.3 - - - +
90B ALA* 1.3 55.3 + - - +
91B GLN 3.3 9.7 + - - +
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Residues in contact with ALA 90 (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 ARG* 3.8 46.1 + - + +
35B VAL* 4.8 11.2 - - + -
86B ALA 2.9 13.1 + - - +
87B ILE* 3.1 11.3 + - + +
89B ALA* 1.3 76.2 - - - +
91B GLN* 1.3 71.5 + - - +
92B PRO* 3.9 2.9 - - - +
181B LEU* 4.7 9.1 - - + +
201E VAL* 5.4 3.1 - - + +
203E PHE* 4.3 1.6 - - - -
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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