Contacts of the strand formed by residues 28 - 37 (chain B) in PDB entry 1R37
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 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B PRO* 4.1 3.1 - - - -
26B PRO 3.8 0.4 - - - +
27B GLN* 1.3 81.5 - - - +
29B LEU* 1.3 65.2 + - - +
30B ILE* 3.9 24.0 - - + -
74B ILE* 4.1 7.2 - - + -
76B GLU 3.6 10.5 - - - +
77B VAL* 3.9 11.0 - - + -
81B VAL* 3.8 11.9 - - + -
131B ILE* 3.6 2.5 - - - -
132B VAL* 2.7 47.3 + - + +
135B TYR* 3.5 34.3 - - + +
138B MET* 3.9 14.1 - - + -
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Residues in contact with LEU 29 (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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20B VAL* 3.9 17.5 - - + -
21B PRO* 3.8 26.7 - - + +
23B PRO* 3.9 16.7 - - + +
28B VAL* 1.3 71.7 - - - +
30B ILE* 1.3 55.6 + - - +
74B ILE* 3.8 2.8 - - - -
75B GLU* 2.8 54.0 + - + +
76B GLU* 2.6 27.4 + - + +
129B TYR* 3.9 22.9 - - + -
130B VAL 3.8 13.2 - - - +
131B ILE* 3.9 13.9 - - + -
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Residues in contact with ILE 30 (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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28B VAL* 3.9 9.2 - - + -
29B LEU* 1.3 73.4 - - - +
31B LYS* 1.3 65.7 + - - +
32B VAL* 3.4 2.9 + - + +
70B ILE* 5.1 1.1 - - + -
71B ALA 4.7 1.3 - - - -
72B GLY* 3.5 30.5 - - - +
73B LYS 3.4 1.6 - - - +
74B ILE* 3.5 36.6 - - + +
90B VAL* 3.7 17.9 - - + -
92B VAL* 4.4 8.3 - - + -
129B TYR* 3.2 9.5 - - - +
130B VAL* 3.0 47.5 + - + +
132B VAL* 3.6 26.2 - - + -
138B MET* 4.2 1.8 - - - -
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Residues in contact with LYS 31 (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 LEU 4.2 0.8 + - - -
30B ILE* 1.3 71.8 - - - +
32B VAL* 1.3 66.5 + - - +
33B GLU* 3.4 28.1 + - - +
72B GLY* 3.2 1.0 - - - -
73B LYS* 2.6 57.1 + - + +
75B GLU* 4.0 17.8 - - - +
128B GLU 3.7 7.6 - - - +
129B TYR* 3.7 29.8 - - + +
347B PRO* 5.6 3.2 + - - -
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Residues in contact with VAL 32 (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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30B ILE* 4.5 0.9 - - + -
31B LYS* 1.3 75.2 + - - +
33B GLU* 1.3 66.5 + - - +
34B ALA 3.6 27.6 - - - +
35B ALA* 4.3 1.8 - - + -
70B ILE* 5.2 1.3 - - + -
71B ALA 4.0 5.2 - - - +
72B GLY* 4.4 1.1 - - - -
125B ALA* 3.6 28.5 - - + +
127B ALA 3.4 24.0 - - - +
128B GLU 3.0 12.8 + - - +
129B TYR 4.2 5.6 - - - -
130B VAL* 3.8 28.9 - - + -
347B PRO* 4.3 22.7 - - + +
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Residues in contact with GLU 33 (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 LYS* 3.7 28.9 + - - +
32B VAL* 1.3 80.2 - - - +
34B ALA* 1.3 63.7 + - - +
71B ALA 3.0 6.3 + - - +
72B GLY* 3.8 10.8 - - - -
73B LYS* 3.0 40.1 + - - +
89B LEU* 4.1 9.2 - - + -
146B ALA* 3.5 22.4 - - + +
147B VAL* 4.7 2.4 - - - +
345B LEU 4.8 0.7 - - - -
346B ILE* 4.1 17.7 - - - +
347B PRO* 4.9 8.2 - - - +
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Residues in contact with ALA 34 (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 VAL* 3.6 9.8 - - - +
33B GLU* 1.3 83.1 - - - +
35B ALA* 1.3 61.3 + - - +
69B GLU 3.7 1.9 - - - +
70B ILE* 4.1 0.9 - - - -
71B ALA* 3.2 25.7 + - + +
146B ALA* 3.4 34.3 - - + +
147B VAL* 3.8 11.7 - - + -
150B ALA* 3.8 7.1 - - + +
344B VAL* 3.9 7.2 - - + -
345B LEU 3.4 8.1 - - - -
346B ILE* 5.0 0.2 - - + -
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Residues in contact with ALA 35 (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 VAL* 4.3 2.7 - - + -
34B ALA* 1.3 75.5 - - - +
36B GLY* 1.3 65.1 + - - +
67B GLY* 5.5 0.4 - - - -
69B GLU 3.2 5.6 - - - +
125B ALA* 3.7 32.8 - - + +
126B TYR* 3.9 17.5 - - + -
344B VAL* 3.8 1.7 - - - +
345B LEU* 2.8 46.3 + - + +
347B PRO* 4.9 2.0 - - + -
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Residues in contact with GLY 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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35B ALA* 1.3 76.1 - - - +
37B VAL* 1.3 62.2 + - - -
38B CYS* 3.9 1.6 + - - +
41B ASP* 4.6 1.0 - - - +
67B GLY* 4.8 1.2 - - - -
68B HIS* 4.8 0.5 + - - -
69B GLU* 3.0 46.6 + - - +
126B TYR* 3.6 13.0 + - - -
150B ALA* 4.0 6.5 - - - +
151B PRO* 5.0 0.4 - - - -
343B GLN 3.7 8.1 - - - -
344B VAL* 4.3 9.6 - - - -
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Residues in contact with VAL 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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35B ALA 4.1 0.2 - - - +
36B GLY* 1.3 73.3 - - - -
38B CYS* 1.3 62.5 + - - +
69B GLU* 3.8 0.4 + - - -
126B TYR* 3.4 17.3 - - + +
327B ALA 5.5 0.7 - - - +
330B ALA* 4.0 17.9 - - + +
331B ILE* 4.0 21.8 - - + -
334B LEU* 3.8 22.2 - - + +
342B ARG* 3.2 23.8 + - - -
343B GLN* 3.0 25.4 + - - +
345B LEU* 3.6 38.4 - - + -
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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