Contacts of the strand formed by residues 53 - 58 (chain B) in PDB entry 6MOL
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 TYR 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B TRP* 4.0 12.8 - + + -
42B GLU* 2.5 44.3 + - - -
51B GLY* 4.2 9.7 - - - +
52B GLN* 1.3 95.7 - - + +
54B SER* 1.3 60.9 + - - +
69B LEU* 3.7 28.3 - - + +
81B PHE* 4.4 18.2 - + - -
100B VAL* 4.0 11.9 - - + -
101B THR 3.3 7.0 - - - +
102B ALA* 4.0 25.6 - - + -
108B ARG* 3.6 34.8 - - + -
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Residues in contact with SER 54 (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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329A TRP* 5.5 1.2 - - - -
53B TYR* 1.3 75.3 - - - +
55B PHE* 1.3 60.4 + - - +
56B SER* 4.4 4.0 + - - -
66B LEU* 4.6 18.8 - - - -
69B LEU* 5.5 0.7 - - - -
99B ARG 3.6 1.9 - - - +
100B VAL* 3.5 6.1 - - - -
101B THR* 2.8 49.6 + - - -
102B ALA 4.8 2.2 + - - -
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.4 10.5 - - + -
38B CYS* 3.8 31.4 - - + -
40B TRP* 4.6 3.6 - + - -
53B TYR 4.3 0.8 + - - -
54B SER* 1.3 72.5 - - - +
56B SER* 1.3 64.6 + - - +
57B TYR* 4.4 4.0 - + + -
66B LEU* 3.2 11.0 - - - +
67B CYS* 3.1 53.4 + - + +
69B LEU* 4.2 24.4 - - + +
83B CYS* 3.8 9.2 - - + -
85B LEU* 3.9 16.8 - - + -
98B LEU* 3.7 35.7 - - + -
99B ARG 3.9 1.6 - - - -
100B VAL* 3.7 27.6 - - + +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A TRP* 3.6 22.5 - - - -
54B SER* 4.4 6.4 + - - -
55B PHE* 1.3 79.3 + - - +
57B TYR* 1.3 61.0 + - - +
64B TRP* 3.8 24.1 - - - -
65B LYS 3.4 7.2 - - - -
66B LEU* 3.8 17.0 - - - +
97B GLU 3.8 0.3 - - - +
98B LEU* 3.4 4.3 - - - +
99B ARG 2.9 40.8 + - - -
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Residues in contact with TYR 57 (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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55B PHE* 4.4 2.2 - + + -
56B SER* 1.3 75.1 - - - +
58B GLN* 1.3 66.3 + - - +
59B LEU* 5.1 4.3 - - + -
63B PRO 4.3 0.3 - - - +
64B TRP* 3.8 3.3 - - - -
65B LYS* 3.0 65.1 + - + +
66B LEU 3.9 17.8 + - - -
67B CYS* 4.0 20.9 - - + -
85B LEU* 3.9 22.9 - - + -
86B PRO* 3.6 16.8 - - + +
89B ASP* 2.7 42.3 + - + -
96B LEU* 4.1 9.6 - - + -
97B GLU 3.3 6.1 - - - -
98B LEU* 3.7 23.3 - - + -
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Residues in contact with GLN 58 (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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303A LYS* 3.5 24.0 - - - +
306A ARG* 2.6 36.7 + - - -
501A GOL 3.8 10.2 + - - -
57B TYR* 1.3 78.3 - - - +
59B LEU* 1.3 78.2 + - - +
62B GLU 2.7 29.5 + - - +
63B PRO 4.0 7.0 - - - +
64B TRP* 3.7 38.8 - - + -
95B PRO 4.0 0.9 - - - +
96B LEU* 3.3 11.0 - - - +
97B GLU* 3.1 28.4 + - + +
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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