Contacts of the strand formed by residues 59 - 66 (chain B) in PDB entry 1IVV
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 ARG 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.3 9.6 - - - +
45B LEU* 2.8 51.5 + - + +
57B ASP* 2.9 40.3 + - - +
58B ARG* 1.3 72.8 - - - +
60B PHE* 1.3 57.8 + - - +
76B THR* 4.2 9.8 - - + +
77B VAL 3.1 12.6 - - - +
78B SER* 4.1 4.3 - - - -
85B ILE* 3.5 46.0 - - - +
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.7 31.9 - - + -
19B GLU* 3.7 33.9 - - + -
20B ILE* 4.6 4.7 - - + -
23B VAL* 3.7 32.5 - - + -
42B LEU* 3.8 22.9 - - + -
43B GLY 3.3 8.5 - - - +
44B VAL* 3.6 30.5 - - + -
45B LEU* 4.3 4.0 - - - +
58B ARG* 4.6 1.3 - - + -
59B ARG* 1.3 80.8 - - - +
61B ARG* 1.3 62.3 + - - +
62B VAL* 4.8 2.4 - - + +
75B VAL 3.8 0.5 - - - +
76B THR* 3.3 4.7 - - - +
77B VAL* 2.9 35.7 + - + +
79B VAL* 3.7 19.5 - - + -
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Residues in contact with ARG 61 (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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41B TYR* 3.6 16.3 + - + -
42B LEU* 3.4 4.0 - - - +
43B GLY 2.9 31.3 + - - +
45B LEU* 3.9 20.5 - - + +
60B PHE* 1.3 73.4 - - - +
62B VAL* 1.3 65.6 + - - +
63B PHE* 3.4 21.7 - - + -
74B GLU* 2.9 37.0 + - + +
75B VAL 3.3 8.1 - - - +
76B THR* 3.8 13.5 - - - +
252B ARG* 5.0 0.2 - - - +
551B ARG* 3.8 34.4 - - - +
552B TYR* 3.8 19.4 + - - -
556B ASP* 3.0 39.6 + - - -
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Residues in contact with VAL 62 (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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23B VAL* 4.1 16.4 - - + -
27B LEU* 4.3 10.8 - - + -
39B ILE* 3.4 35.0 - - + -
41B TYR 3.2 11.9 - - - +
42B LEU* 4.0 19.7 - - + -
60B PHE 4.8 3.1 - - - +
61B ARG* 1.3 82.1 - - - +
63B PHE* 1.3 75.2 + - - +
64B ILE* 3.7 17.0 - - + -
73B GLN 3.8 0.3 - - - +
74B GLU* 3.4 0.9 - - - +
75B VAL* 2.7 40.7 + - + +
77B VAL* 5.4 1.8 - - + -
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.6 4.0 - - - -
40B ALA* 2.8 29.2 + - + -
41B TYR* 2.9 42.5 + + + +
61B ARG* 3.4 38.4 - - + -
62B VAL* 1.3 81.6 - - - +
64B ILE* 1.3 60.3 + - - +
73B GLN 3.6 4.9 - - - -
74B GLU* 3.5 25.8 - - + -
98B LEU* 3.9 17.3 - - + -
99B PRO* 4.0 15.0 - - + -
252B ARG* 4.1 7.6 - - - -
556B ASP* 3.7 19.3 - - + -
557B PHE* 3.5 29.2 - + - -
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Residues in contact with ILE 64 (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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27B LEU* 4.1 22.0 - - + -
32B LEU* 3.9 20.9 - - + +
33B LEU* 4.2 4.3 - - + -
37B LYS* 3.6 39.5 + - + +
38B ARG 3.4 7.2 - - - +
39B ILE* 4.2 4.9 - - + -
62B VAL* 3.7 17.5 - - + -
63B PHE* 1.3 74.3 - - - +
65B HIS* 1.3 61.4 + - - +
72B PRO* 3.1 23.4 - - - +
73B GLN* 2.8 26.1 + - + +
75B VAL* 3.8 27.6 - - + -
98B LEU* 3.6 3.1 - - - +
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Residues in contact with HIS 65 (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 GLU 3.7 0.2 - - - +
37B LYS* 3.2 6.0 - - - +
38B ARG* 2.6 41.2 + - + +
40B ALA* 4.5 4.7 - - + -
63B PHE 4.0 0.2 + - - -
64B ILE* 1.3 77.7 - - - +
66B ASP* 1.3 84.0 + - - +
67B VAL* 4.0 17.7 - - + +
70B ALA 5.8 0.2 + - - -
72B PRO* 4.3 4.9 - - - +
98B LEU* 3.6 17.5 - - + +
101B LEU* 3.3 29.6 - - + -
104B GLU* 3.6 9.9 + - - +
151B ARG* 3.3 37.1 + - - +
182B VAL* 3.9 12.3 - - + +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 3.4 12.2 - - - +
37B LYS* 2.8 35.2 + - - +
64B ILE 4.1 0.2 + - - -
65B HIS* 1.3 92.1 + - - +
67B VAL* 1.3 62.8 + - - +
68B SER* 2.6 41.3 + - - -
69B GLY* 3.1 12.1 + - - -
70B ALA* 3.3 39.1 + - - +
71B ARG 4.4 2.0 - - - +
72B PRO* 4.9 2.0 - - + +
182B VAL* 4.6 0.9 - - - +
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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