Contacts of the strand formed by residues 60 - 68 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.3 6.6 - - - +
35A ALA* 3.1 39.4 + - + +
36A PRO 3.5 2.9 - - - +
37A CYS* 3.2 17.8 - - - +
59A HIS* 1.3 92.7 - - + +
61A ALA* 1.3 61.6 + - - +
119A VAL* 3.9 2.9 - - - +
146A VAL* 4.0 19.8 - - - +
149A PRO* 4.3 6.3 - - + -
150A ASP* 3.4 28.6 - - + +
151A MET* 3.6 8.9 + - - +
346A LYS* 2.9 39.9 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.7 2.0 - - + -
33A ALA 3.3 5.8 - - - -
34A VAL* 3.8 11.7 - - + -
59A HIS 4.1 1.6 + - - -
60A GLU* 1.3 76.5 - - - +
62A VAL* 1.3 63.1 + - - +
63A GLY 4.2 0.7 - - - -
83A VAL* 3.4 32.5 + - + +
119A VAL* 3.7 30.7 - - + -
124A PHE* 4.2 16.2 - - + -
146A VAL* 4.1 3.2 - - - +
149A PRO* 3.8 6.0 - - - +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.9 1.5 - - - -
32A LEU* 2.8 24.8 + - + +
33A ALA* 2.9 20.9 + - + +
61A ALA* 1.3 77.2 - - - +
63A GLY* 1.3 62.4 + - - +
81A VAL 3.4 14.1 - - - +
82A VAL* 4.2 14.6 - - + -
83A VAL 4.7 0.2 - - - +
136A LEU* 3.6 27.1 - - + -
142A LEU* 3.9 16.2 - - + +
145A ALA* 3.7 37.5 - - + +
146A VAL* 3.7 9.1 - - + +
149A PRO* 4.6 0.7 - - + -
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.7 15.2 - - - +
30A ARG 3.1 14.6 - - - -
31A PRO* 4.0 2.2 - - - -
32A LEU* 3.6 12.4 - - - +
61A ALA 4.2 0.6 - - - -
62A VAL* 1.3 74.7 - - - +
64A GLU* 1.3 60.2 + - - +
80A ARG* 3.9 2.3 - - - -
81A VAL* 3.0 33.0 + - - +
83A VAL* 4.5 3.0 - - - +
124A PHE* 5.1 0.6 - - - -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.5 3.1 - - - +
30A ARG* 2.9 64.7 + - + +
32A LEU* 4.0 17.0 - - + +
63A GLY* 1.3 75.0 - - - -
65A VAL* 1.3 75.2 + - - +
66A VAL* 3.4 6.8 + - - +
78A GLY* 3.5 25.2 - - - +
79A ASP 3.3 13.9 - - - +
80A ARG* 5.0 5.1 + - + +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.6 2.9 - - + -
28A ILE 4.0 5.4 - - - +
29A VAL* 4.5 4.5 - - + +
64A GLU* 1.3 76.2 - - - +
66A VAL* 1.3 59.0 + - - +
67A GLU 3.9 9.6 - - - +
68A VAL* 3.6 28.7 - - + -
75A PHE* 4.6 5.2 - - + -
76A LYS 3.5 24.2 - - - +
78A GLY 2.7 29.9 + - - -
79A ASP* 2.9 12.9 + - + +
81A VAL* 3.7 35.2 - - + -
133A LEU* 4.1 14.8 - - + -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS* 5.7 2.5 - - - +
28A ILE* 3.2 26.9 + - + +
30A ARG* 3.7 29.4 - - + +
64A GLU* 3.4 14.8 + - - +
65A VAL* 1.3 77.6 - - - +
67A GLU* 1.3 63.2 + - + +
77A PRO* 3.3 22.9 - - - +
123A PHE* 3.9 24.9 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS* 5.3 9.2 + - - -
22A PRO* 3.4 30.7 - - + +
27A ALA* 3.3 6.4 - - - +
28A ILE* 2.9 40.8 + - + +
65A VAL* 3.8 1.5 - - - +
66A VAL* 1.3 84.9 - - + +
68A VAL* 1.3 75.5 + - - +
77A PRO* 4.3 4.9 - - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 5.0 3.6 - - - +
26A ASP 3.7 5.6 - - - -
27A ALA* 4.0 7.6 - - + -
65A VAL* 3.6 20.6 - - + -
67A GLU* 1.3 89.5 - - - +
69A GLY* 1.3 71.1 + - - +
72A VAL* 3.8 21.8 - - + +
75A PHE* 3.4 28.3 - - + +
76A LYS* 4.4 1.8 - - - +
77A PRO* 4.2 15.7 - - + +
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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