Contacts of the strand formed by residues 61 - 67 (chain B) in PDB entry 1B70
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 LEU 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B PRO* 3.3 6.2 - - - +
56B ILE* 2.7 38.7 + - + +
59B THR* 2.9 19.8 + - - +
60B ARG* 1.3 95.6 - - + +
62B LYS* 1.3 61.8 + - - +
75B VAL* 3.6 25.6 - - + -
76B SER 3.6 9.6 - - - +
77B GLY* 4.5 9.9 - - - -
108B ILE* 4.0 14.6 - - + -
109B GLN* 4.4 11.2 - - + -
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 4.5 15.8 + - + +
54B HIS 3.1 9.6 - - - +
55B PRO* 4.3 22.8 - - + +
56B ILE* 3.8 5.2 - - - -
60B ARG 5.4 1.8 - - - +
61B LEU* 1.3 80.8 - - - +
63B ARG* 1.3 60.3 + - - +
64B LEU* 3.8 15.8 + - + +
75B VAL* 3.2 5.0 - - - +
76B SER* 2.8 37.8 + - - +
77B GLY 6.3 0.2 - - - -
78B ALA 4.8 7.4 - - - +
79B GLU* 4.8 4.8 + - - +
81B ALA* 3.1 33.5 + - + -
82B ARG* 4.5 5.3 - - - +
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Residues in contact with ARG 63 (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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52B GLU 3.9 0.2 - - - +
53B ALA* 3.7 0.7 - - - -
54B HIS* 2.5 78.8 + - - +
56B ILE* 3.6 17.2 - - + +
62B LYS* 1.3 72.5 - - - +
64B LEU* 1.3 62.0 + - - +
65B VAL* 3.7 16.7 + - - +
73B GLU* 3.0 41.9 + - + +
74B VAL 3.5 7.0 - - - +
75B VAL* 4.4 4.7 - - + +
111B VAL* 4.8 12.8 - - + -
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Residues in contact with LEU 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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50B VAL* 4.3 10.8 - - + -
52B GLU 3.3 3.8 - - - +
53B ALA* 3.7 27.4 - - + -
62B LYS* 4.0 19.1 - - + +
63B ARG* 1.3 77.3 - - - +
65B VAL* 1.3 62.0 + - - +
66B LEU* 3.9 15.7 + - + -
72B VAL 3.7 0.2 - - - +
73B GLU* 3.2 9.0 - - - +
74B VAL* 2.8 48.7 + - + +
76B SER* 3.7 24.2 - - - -
81B ALA* 4.3 19.1 - - + -
82B ARG 5.1 0.2 - - - +
87B VAL* 6.0 0.7 - - + -
117B ALA* 5.3 3.6 - - + -
132B LEU* 4.5 9.9 - - + -
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Residues in contact with VAL 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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51B LEU* 2.9 37.1 + - + +
52B GLU* 2.7 36.8 + - + +
54B HIS* 4.1 6.3 - - + +
63B ARG* 3.7 28.0 - - - +
64B LEU* 1.3 76.1 - - - +
66B LEU* 1.3 64.0 + - - +
71B THR* 3.8 24.2 - - + -
72B VAL 3.5 3.6 - - - +
73B GLU* 4.4 7.9 - - + -
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Residues in contact with LEU 66 (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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48B ALA* 4.3 13.5 - - + -
49B ARG 3.4 3.6 - - - +
50B VAL* 3.5 33.7 - - + +
51B LEU* 3.6 5.4 - - - -
64B LEU* 4.0 11.4 - - + +
65B VAL* 1.3 83.5 - - - +
67B ASP* 1.3 60.8 + - - +
68B ALA 3.6 0.6 + - - -
71B THR* 3.3 8.7 - - - +
72B VAL* 2.6 54.0 + - + +
74B VAL* 3.6 30.7 - - + -
87B VAL* 4.3 11.4 - - + -
89B LEU* 4.1 24.9 - - + -
117B ALA* 5.5 1.3 - - + -
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Residues in contact with ASP 67 (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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48B ALA* 3.4 1.8 - - - -
49B ARG* 2.9 45.7 + - + -
51B LEU* 3.4 27.7 - - + +
66B LEU* 1.3 72.7 - - - +
68B ALA* 1.3 60.1 + - - +
69B GLY* 3.1 21.3 + - - +
70B ARG 4.4 2.1 - - - +
71B THR* 4.7 3.1 - - - +
142B PRO* 3.2 31.7 - - - +
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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