Contacts of the strand formed by residues 69 - 76 (chain B) in PDB entry 1D1T
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 ALA 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ILE* 4.2 6.7 - - + -
42B ALA 3.4 12.8 - - - +
43B THR* 3.8 2.9 - - - -
67B HIS 3.3 4.8 + - - -
68B GLU* 1.3 76.3 - - - +
70B THR* 1.3 64.3 + - - +
90B ILE* 3.4 14.9 - - - +
91B PRO* 2.9 24.3 - - + +
145B THR* 3.4 34.3 - - + -
170B CYS* 3.8 8.8 + - - -
173B GLY* 4.8 1.8 - - - -
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Residues in contact with THR 70 (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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40B ILE* 3.9 4.5 - - - +
41B LEU* 3.0 21.6 + - + -
42B ALA 3.0 11.6 + - - +
69B ALA* 1.3 74.2 + - - +
71B GLY* 1.3 62.1 + - - +
88B LYS* 4.2 11.0 - - + -
89B VAL 3.6 9.6 - - - +
90B ILE* 4.5 1.4 - - + +
91B PRO* 4.8 1.3 - - - -
160B ILE* 4.0 12.6 - - + -
166B PRO* 2.9 48.1 + - + -
169B VAL* 3.5 14.3 + - + +
170B CYS* 3.0 19.3 + - - +
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Residues in contact with GLY 71 (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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38B ILE* 3.8 8.7 - - - +
39B LYS 3.0 15.7 - - - -
40B ILE* 4.3 0.7 - - - -
41B LEU* 3.9 7.4 - - - -
70B THR* 1.3 76.8 - - - +
72B ILE* 1.3 60.9 + - - +
88B LYS* 3.4 10.9 - - - +
89B VAL* 2.8 38.2 + - - -
91B PRO* 4.8 0.2 - - - +
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Residues in contact with ILE 72 (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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38B ILE* 3.6 3.1 - - - +
39B LYS* 2.9 39.0 + - + +
41B LEU* 3.4 26.7 - - + -
71B GLY* 1.3 73.7 - - - +
73B VAL* 1.3 68.4 + - - +
74B GLU* 3.2 0.7 + - - -
86B GLY* 3.4 29.8 - - - +
87B ASP 3.2 2.9 - - - -
88B LYS* 3.7 40.2 - - + -
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Residues in contact with VAL 73 (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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36B VAL* 3.8 16.2 - - + -
37B ARG 3.7 6.3 - - - +
38B ILE* 4.5 1.3 - - - +
72B ILE* 1.3 72.2 - - - +
74B GLU* 1.3 61.4 + - - +
75B SER 3.4 31.9 - - - +
76B ILE* 3.7 16.6 - - + -
83B VAL* 4.2 6.7 - - + -
84B LYS 3.5 19.1 - - - +
85B PRO* 3.4 2.5 - - + +
86B GLY* 2.8 26.7 + - - -
87B ASP* 2.8 15.4 + - + +
89B VAL* 3.5 31.9 - - + -
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Residues in contact with GLU 74 (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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2B THR* 2.8 45.7 + - - +
3B ALA* 3.4 4.7 + - - +
7B ILE* 3.9 4.3 - - - -
37B ARG* 2.7 37.8 + - - +
39B LYS* 4.6 4.9 - - + +
72B ILE* 3.2 4.9 + - - +
73B VAL* 1.3 75.0 - - - +
75B SER* 1.3 87.8 + - - +
85B PRO* 3.8 11.3 - - - +
149B TYR* 3.9 30.7 - - + -
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Residues in contact with SER 75 (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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3B ALA* 4.3 19.1 - - - -
4B GLY 5.1 0.4 + - - -
31B PRO* 3.8 17.6 - - - +
36B VAL 3.7 0.5 - - - -
37B ARG* 2.9 31.1 + - - +
73B VAL* 3.4 8.5 - - - +
74B GLU* 1.3 107.5 + - - +
76B ILE* 1.3 67.7 + - - +
85B PRO* 4.2 8.1 - - - -
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Residues in contact with ILE 76 (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 PRO* 3.8 5.4 - - - +
35B GLU 4.0 4.0 - - - -
36B VAL* 4.6 1.6 - - + -
73B VAL* 3.7 18.6 - - + -
75B SER* 1.3 81.2 - - - +
77B GLY* 1.3 64.8 + - - +
80B VAL* 3.9 27.6 - - + +
83B VAL* 3.7 37.5 - - + +
84B LYS* 4.0 7.4 - - + -
85B PRO* 4.2 17.4 - - + +
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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