Contacts of the strand formed by residues 28 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PRO* 4.1 3.6 - - - -
26A PRO 3.9 0.4 - - - +
27A GLN* 1.3 80.6 - - - +
29A LEU* 1.3 63.7 + - - +
30A ILE* 3.9 25.1 - - + -
74A ILE* 4.1 9.2 - - + -
76A GLU 3.6 9.6 - - - +
77A VAL* 4.1 5.8 - - + -
81A VAL* 3.8 12.1 - - + -
131A ILE* 3.6 2.2 - - - -
132A VAL* 2.8 44.3 + - + +
135A TYR* 3.5 33.4 - - + -
138A MET* 3.7 22.2 - - + -
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Residues in contact with LEU 29 (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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20A VAL* 3.8 17.9 - - + -
21A PRO* 3.7 22.9 - - + +
23A PRO* 3.9 18.2 - - + +
28A VAL* 1.3 71.5 - - - +
30A ILE* 1.3 55.1 + - - +
74A ILE* 3.8 2.6 - - - -
75A GLU* 2.8 52.9 + - + -
76A GLU* 2.6 29.1 + - + +
129A TYR* 3.8 26.2 - - + -
130A VAL 3.9 7.9 - - - +
131A ILE* 3.8 21.5 - - + -
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Residues in contact with ILE 30 (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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28A VAL* 3.9 8.3 - - + -
29A LEU* 1.3 73.6 - - - +
31A LYS* 1.3 66.0 + - - +
32A VAL* 3.4 4.1 + - + +
70A ILE* 5.0 3.6 - - + -
71A ALA 4.7 1.6 - - - -
72A GLY* 3.6 29.8 - - - +
73A LYS 3.4 1.1 - - - +
74A ILE* 3.5 36.6 - - + +
90A VAL* 3.7 17.0 - - + -
92A VAL* 4.3 6.7 - - + -
129A TYR* 3.2 8.9 - - - +
130A VAL* 2.9 48.3 + - + +
132A VAL* 3.6 26.2 - - + -
138A MET* 4.2 0.9 - - - -
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Residues in contact with LYS 31 (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 LEU 4.2 0.6 + - - -
30A ILE* 1.3 72.5 - - - +
32A VAL* 1.3 67.5 + - - +
33A GLU* 3.4 28.8 + - - +
72A GLY* 3.2 0.7 - - - -
73A LYS* 2.6 56.2 + - + +
75A GLU* 4.0 18.3 - - - +
128A GLU 3.7 8.5 - - - +
129A TYR* 3.7 30.0 - - + +
347A PRO* 5.5 4.0 + - - -
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Residues in contact with VAL 32 (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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30A ILE* 4.5 1.3 - - + -
31A LYS* 1.3 76.1 + - - +
33A GLU* 1.3 67.0 + - - +
34A ALA* 3.6 26.7 - - - +
35A ALA* 4.3 2.2 - - + -
70A ILE* 5.3 0.9 - - + -
71A ALA 4.0 6.3 - - - +
72A GLY* 4.4 0.7 - - - -
125A ALA* 3.6 29.2 - - + +
127A ALA 3.3 24.2 - - - +
128A GLU* 3.0 12.5 + - - +
129A TYR 4.2 2.7 - - - -
130A VAL* 3.8 27.8 - - + -
347A PRO* 4.3 22.3 - - + +
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Residues in contact with GLU 33 (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 LYS* 3.6 28.7 + - - +
32A VAL* 1.3 80.2 - - - +
34A ALA* 1.3 64.2 + - - +
71A ALA 3.1 7.0 + - - +
72A GLY* 3.8 10.3 - - - -
73A LYS* 3.0 37.8 - - + +
89A LEU* 4.2 9.4 - - + -
146A ALA* 3.5 23.2 - - + +
147A VAL* 4.7 2.1 - - - +
345A LEU 4.9 0.4 - - - -
346A ILE* 4.1 17.4 - - - +
347A PRO* 4.9 7.7 - - - +
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Residues in contact with ALA 34 (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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32A VAL* 3.6 8.7 - - - +
33A GLU* 1.3 81.8 - - - +
35A ALA* 1.3 62.6 + - - +
69A GLU 3.7 2.3 - - - +
70A ILE* 4.1 0.7 - - - -
71A ALA* 3.2 25.9 + - + +
125A ALA* 4.7 0.2 - - - +
146A ALA* 3.3 33.4 - - + +
147A VAL* 3.7 12.6 - - + -
150A ALA* 3.8 4.6 - - + +
344A VAL* 3.9 9.9 - - + -
345A LEU 3.4 7.9 - - - -
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Residues in contact with ALA 35 (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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32A VAL* 4.3 2.5 - - + -
34A ALA* 1.3 75.3 - - - +
36A GLY* 1.3 66.4 + - - +
67A GLY* 5.5 0.2 - - - -
69A GLU 3.2 6.7 - - - +
125A ALA* 3.7 33.2 - - + +
126A TYR* 3.9 17.9 - - + -
344A VAL* 3.8 1.7 - - - +
345A LEU* 2.8 47.6 + - + +
347A PRO* 4.9 1.8 - - + -
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Residues in contact with GLY 36 (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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35A ALA* 1.3 76.1 - - - +
37A VAL* 1.3 60.2 + - - -
38A CYS 3.9 1.7 + - - -
41A ASP* 4.6 1.0 - - - +
67A GLY* 4.8 1.4 - - - -
68A HIS* 4.8 0.9 + - - -
69A GLU* 3.0 45.5 + - - +
126A TYR* 3.6 13.2 + - - -
150A ALA* 4.0 6.3 - - - +
151A PRO* 5.0 0.2 - - - -
343A GLN 3.7 8.5 - - - -
344A VAL* 4.2 9.6 - - - -
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Residues in contact with VAL 37 (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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35A ALA 4.2 0.4 - - - +
36A GLY* 1.3 71.4 - - - -
38A CYS* 1.3 63.4 + - - +
69A GLU* 3.7 0.8 + - - -
126A TYR* 3.4 17.0 - - - +
327A ALA* 5.5 0.7 - - - +
330A ALA* 4.0 17.9 - - + +
331A ILE* 4.0 22.9 - - + -
334A LEU* 3.8 21.7 - - + +
342A ARG* 3.5 23.6 + - - -
343A GLN* 3.0 25.5 + - + +
345A LEU* 3.6 37.9 - - + -
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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