Contacts of the strand formed by residues 60 - 68 (chain B) in PDB entry 7UUT
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 GLU 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.3 6.2 - - - +
35B ALA* 3.2 37.6 + - + +
36B PRO 3.5 2.6 - - - +
37B CYS* 3.1 18.0 - - - +
59B HIS* 1.3 93.1 - - + +
61B ALA* 1.3 61.9 + - - +
119B VAL* 3.7 3.1 - - - +
146B VAL* 3.9 22.8 - - - +
147B MET* 4.8 0.2 - - - +
149B PRO* 4.1 7.2 - - + -
150B ASP* 3.5 25.6 - - + +
151B MET* 3.8 7.4 + - - +
346B LYS* 2.8 41.2 + - - -
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Residues in contact with ALA 61 (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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33B ALA 3.3 5.2 - - - -
34B VAL* 3.8 9.9 - - + -
59B HIS 4.1 1.8 + - - -
60B GLU* 1.3 77.4 - - - +
62B VAL* 1.3 64.7 + - - +
63B GLY 4.2 0.2 - - - -
83B VAL* 3.3 32.6 + - + +
119B VAL* 3.6 31.9 - - + -
124B PHE* 4.0 16.4 - - + -
146B VAL* 4.1 2.0 - - - +
149B PRO* 3.9 9.8 - - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PRO* 3.6 2.8 - - - +
32B LEU* 2.6 32.1 + - + -
33B ALA* 2.8 19.9 + - + +
61B ALA* 1.3 75.5 - - - +
63B GLY* 1.3 59.3 + - - +
81B VAL 3.3 15.7 - - - +
82B VAL* 4.4 7.6 - - + -
136B LEU* 3.6 24.5 - - + -
142B LEU* 3.7 20.4 - - + +
145B ALA* 3.6 17.5 - - + +
146B VAL* 3.6 32.5 - - + +
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Residues in contact with GLY 63 (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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29B VAL* 3.6 15.7 - - - +
30B ARG 3.1 12.8 - - - -
31B PRO* 3.9 1.8 - - - -
32B LEU* 3.6 12.2 - - - +
61B ALA 4.2 0.8 + - - -
62B VAL* 1.3 76.5 - - - +
64B GLU* 1.3 61.7 + - - -
80B ARG* 3.5 4.3 - - - +
81B VAL* 2.9 33.6 + - - +
83B VAL* 4.7 1.6 - - - +
124B PHE* 5.2 0.7 - - - -
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Residues in contact with GLU 64 (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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29B VAL* 3.5 3.5 - - - +
30B ARG* 2.7 76.9 + - + +
32B LEU* 3.9 15.7 - - + +
63B GLY* 1.3 74.3 - - - +
65B VAL* 1.3 74.5 + - - +
66B VAL* 3.4 6.2 + - - +
78B GLY* 3.9 29.5 - - - +
79B ASP 3.4 5.2 - - - +
80B ARG* 5.0 4.4 - - + +
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Residues in contact with VAL 65 (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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27B ALA* 4.5 2.7 - - + -
28B ILE 3.8 6.1 - - - +
29B VAL* 4.4 4.3 - - + +
64B GLU* 1.3 76.1 - - - +
66B VAL* 1.3 61.3 + - - +
67B GLU 4.0 7.6 - - - +
68B VAL* 3.6 30.3 - - + -
75B PHE* 4.6 4.5 - - + -
76B LYS 3.5 23.6 - - - +
77B PRO* 3.3 0.2 - - - +
78B GLY 2.7 27.9 + - - -
79B ASP* 2.9 24.2 + - + +
81B VAL* 3.7 26.7 - - + -
133B LEU* 4.2 14.6 - - + -
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Residues in contact with VAL 66 (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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19B LYS* 4.6 7.9 - - - +
28B ILE* 2.9 40.2 + - + +
29B VAL 4.4 0.4 - - - +
30B ARG* 3.8 28.3 - - + +
64B GLU* 3.7 13.5 - - - +
65B VAL* 1.3 78.9 - - - +
67B GLU* 1.3 63.9 + - + +
77B PRO* 3.6 19.3 - - - +
123B PHE* 3.9 18.2 - - + -
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Residues in contact with GLU 67 (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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19B LYS* 5.0 9.6 + - - +
20B PRO 4.9 2.1 - - - +
21B ALA* 5.7 0.2 - - - +
22B PRO* 3.4 33.2 - - + +
27B ALA* 3.3 2.9 - - - +
28B ILE* 2.8 42.0 + - + +
65B VAL* 3.8 1.0 - - - +
66B VAL* 1.3 85.1 - - + +
68B VAL* 1.3 73.6 + - - +
77B PRO* 4.5 5.2 - - - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 4.3 5.9 - - - +
26B ASP 3.6 4.9 - - - -
27B ALA* 3.9 11.9 - - + +
65B VAL* 3.6 21.3 - - + -
67B GLU* 1.3 88.9 - - - +
69B GLY* 1.3 70.1 + - - +
72B VAL* 3.8 18.8 - - + +
75B PHE* 3.6 27.8 - - + +
76B LYS* 4.5 0.7 - - - -
77B PRO* 4.3 15.6 - - + +
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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