Contacts of the strand formed by residues 35 - 44 (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 GLU 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 3.7 2.5 - - + -
32B LYS* 3.0 32.6 + - - +
33B THR 3.4 9.5 - - - +
34B LYS* 1.3 79.0 - - - +
36B VAL* 1.3 64.8 + - - +
77B GLY 2.9 23.6 + - - -
80B VAL* 3.2 7.8 - - - +
123B LEU* 3.7 11.3 - - + +
125B ASP* 4.5 7.1 + - - +
129B ARG* 2.8 45.7 + - - -
151B VAL* 3.5 12.9 - - + +
152B VAL 3.2 10.3 - - - +
153B ASP* 3.8 19.0 - - - +
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Residues in contact with VAL 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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31B PRO* 4.1 0.7 - - - -
35B GLU* 1.3 84.1 - - - +
37B ARG* 1.3 61.7 + - - +
38B ILE* 3.8 19.1 + - + +
73B VAL* 3.8 24.9 - - + -
75B SER 3.8 11.2 - - - +
76B ILE* 4.6 2.0 - - + -
80B VAL* 4.1 11.9 - - + -
83B VAL* 3.7 23.6 - - + -
150B THR 3.7 0.5 - - - +
151B VAL* 3.3 5.6 - - - -
152B VAL* 2.8 36.1 + - - +
154B GLU* 4.5 6.5 - - - -
157B VAL* 4.1 20.2 - - + -
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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
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2B THR 3.2 16.4 + - - -
4B GLY 4.1 1.8 - - - +
5B LYS 2.8 27.2 + - - +
7B ILE* 3.5 21.0 - - - +
28B VAL* 2.8 49.0 + - + -
29B ALA 3.3 8.9 + - - -
30B PRO* 3.6 18.8 - - - +
31B PRO* 3.8 15.1 - - + +
36B VAL* 1.3 71.9 - - - +
38B ILE* 1.3 61.0 - - - +
73B VAL* 3.7 3.8 - - - +
74B GLU* 2.7 53.1 + - - +
75B SER* 2.9 20.3 + - - +
149B TYR* 4.4 10.1 - - + -
150B THR 3.3 11.2 - - - +
151B VAL* 4.1 3.6 - - + +
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Residues in contact with ILE 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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36B VAL* 3.9 13.0 - - + +
37B ARG* 1.3 78.5 - - - +
39B LYS* 1.3 76.5 + - - +
40B ILE* 3.9 9.3 + - + -
71B GLY* 3.8 9.0 - - - -
72B ILE 3.6 17.0 - - - +
73B VAL* 4.7 1.1 - - + -
74B GLU 4.8 0.2 - - - -
89B VAL* 3.8 23.3 - - + -
91B PRO* 4.3 18.6 - - + -
149B TYR* 3.2 10.0 - - - +
150B THR* 2.8 42.6 + - + +
152B VAL* 3.8 30.5 - - + -
157B VAL* 4.3 8.5 - - + -
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Residues in contact with LYS 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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38B ILE* 1.3 74.2 - - - +
40B ILE* 1.3 67.9 + - - +
41B LEU* 3.7 17.1 + - + +
71B GLY* 3.0 5.5 - - - -
72B ILE* 2.9 42.3 + - + +
74B GLU* 4.5 4.8 - - + +
148B GLU* 3.3 10.5 - - + +
149B TYR* 3.3 41.7 + - + +
374B PHE* 6.4 0.9 - - - -
239C GLU* 5.6 4.0 + - - -
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Residues in contact with ILE 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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38B ILE* 4.0 21.3 - - + +
39B LYS* 1.3 76.1 - - - +
41B LEU* 1.3 65.6 + - - +
42B ALA 3.7 19.5 - - - +
43B THR* 4.3 0.7 - - - -
69B ALA* 4.2 9.9 - - + -
70B THR 3.9 3.4 - - - +
71B GLY* 4.9 0.7 - - - -
91B PRO* 4.9 5.2 - - + -
145B THR* 3.7 29.4 - - + +
147B THR* 3.2 26.0 - - + +
148B GLU 2.8 13.1 + - - +
150B THR* 4.1 18.6 - - + -
374B PHE* 3.2 43.1 - - + +
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Residues in contact with LEU 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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39B LYS* 4.4 21.5 - - + +
40B ILE* 1.3 78.9 - - - +
42B ALA* 1.3 64.7 + - - +
70B THR* 3.0 7.9 + - + +
71B GLY* 3.9 15.0 - - - +
72B ILE* 3.4 34.5 - - + -
88B LYS* 4.9 1.6 - - - -
166B PRO* 3.8 33.4 - - + -
373B THR* 3.6 5.4 + - - -
374B PHE* 2.9 30.1 + - + +
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Residues in contact with ALA 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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40B ILE* 3.7 2.7 - - - +
41B LEU* 1.3 79.7 - - - +
43B THR* 1.3 62.3 + - - +
69B ALA* 3.4 4.2 - - - +
70B THR 3.0 29.0 + - - +
166B PRO* 3.8 7.4 - - + +
167B GLU* 3.6 38.4 - - + +
170B CYS* 4.4 2.7 - - - -
371B VAL* 3.9 7.6 - - + -
372B LEU 3.2 12.1 - - - +
373B THR* 4.6 3.8 - - - +
374B PHE* 4.7 0.4 - - - -
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Residues in contact with THR 43 (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* 4.3 0.9 - - - -
42B ALA* 1.3 77.3 - - - +
44B GLY* 1.3 61.3 + - - +
68B GLU 2.9 17.3 + - - -
69B ALA* 3.8 4.0 - - - +
145B THR* 2.9 28.3 + - - +
146B PHE* 3.4 29.8 - - + -
170B CYS* 4.5 2.7 - - - -
352B PHE* 5.1 0.4 - - + -
370B THR 4.0 0.3 - - - +
371B VAL* 4.3 2.7 - - - +
372B LEU* 2.8 45.8 + - + +
374B PHE* 4.0 17.0 - - + -
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Residues in contact with GLY 44 (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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43B THR* 1.3 76.5 + - - +
45B ILE* 1.3 63.8 + - - -
46B CYS 3.7 3.3 + - - -
49B ASP* 4.3 1.7 - - - +
67B HIS 5.3 0.2 + - - -
68B GLU* 2.8 39.8 + - - +
146B PHE* 3.5 16.3 - - - -
170B CYS* 4.2 4.8 - - - -
369B ARG* 4.7 2.0 - - - -
370B THR 3.5 8.3 - - - -
371B VAL* 4.4 8.1 - - - -
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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