Contacts of the strand formed by residues 107 - 114 (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 PRO 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A THR* 3.6 39.9 - - + +
364A THR* 3.6 27.4 - - + -
393A ASP* 4.0 15.0 - - + +
394A LEU* 4.2 7.2 - - + +
395A ASN* 3.1 25.5 - - - +
100B VAL 4.4 2.2 - - - +
101B THR* 5.3 0.2 - - - -
102B ALA* 5.7 0.2 - - - -
106B ALA* 1.3 84.1 - - + +
108B ARG* 1.3 61.9 + - - +
109B TYR 6.4 0.4 - - - -
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Residues in contact with ARG 108 (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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405A ARG* 3.3 37.5 + - - +
40B TRP* 3.5 18.8 - - - +
41B GLU 5.6 0.4 + - - -
42B GLU* 3.9 16.0 + - - +
53B TYR* 3.6 34.1 - - + -
100B VAL* 3.1 29.4 + - + +
101B THR 4.7 0.2 - - - +
102B ALA* 4.9 1.3 - - + +
106B ALA 3.5 3.1 + - - +
107B PRO* 1.3 76.5 + - - +
109B TYR* 1.3 120.4 + - + +
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Residues in contact with TYR 109 (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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405A ARG* 4.2 5.2 - - - -
406A MET* 5.9 1.6 - - - -
24B GLU* 3.1 30.7 + - - -
25B GLU* 3.7 3.1 + - - -
26B LEU* 3.4 45.3 - - + -
40B TRP* 3.5 33.1 - + + +
41B GLU 5.1 1.7 + - - -
98B LEU 5.4 0.2 - - - -
99B ARG* 3.5 5.6 - - - +
100B VAL* 2.9 43.2 + - + +
107B PRO* 5.9 0.4 - - - +
108B ARG* 1.3 134.8 + - + +
110B HIS* 1.3 64.7 + - - +
111B ARG* 5.6 2.7 - - - -
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Residues in contact with HIS 110 (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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335A HIS* 6.4 0.4 - - - +
336A LEU* 4.3 6.8 - - + +
339A LEU* 3.2 45.5 - - + +
364A THR* 5.6 2.2 - - - -
369A LEU* 4.2 29.2 - - + +
373A MET* 4.4 3.5 - - - +
97B GLU* 3.3 28.7 + - + -
98B LEU 3.5 8.8 + - - -
99B ARG* 3.0 53.0 + - + -
109B TYR* 1.3 77.0 - - - +
111B ARG* 1.3 69.7 + - - +
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Residues in contact with ARG 111 (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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339A LEU* 4.1 4.9 - - - -
373A MET* 4.4 24.0 - - + +
25B GLU* 4.5 11.8 + - - -
26B LEU* 3.4 50.7 + - + +
27B LEU* 5.5 1.6 - - - +
28B CYS* 3.9 25.7 + - - +
96B LEU 3.8 0.5 - - - +
97B GLU* 4.4 0.2 - - - +
98B LEU* 2.8 40.5 + - + +
109B TYR* 5.6 2.9 - - + -
110B HIS* 1.3 82.7 + - - +
112B VAL* 1.3 63.9 + - - +
113B ILE* 3.4 35.3 - - + +
118B VAL* 5.4 5.3 - - - +
208B PHE* 5.9 4.0 - - - -
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Residues in contact with VAL 112 (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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306A ARG* 3.9 28.5 - - + +
336A LEU* 4.4 4.0 - - + +
339A LEU* 3.6 24.5 - - + +
340A ILE* 4.0 32.7 - - + +
373A MET* 6.1 0.6 - - - +
95B PRO* 4.1 17.9 - - + -
96B LEU 3.4 8.3 - - - +
97B GLU* 3.7 22.9 - - + -
111B ARG* 1.3 78.6 - - - +
113B ILE* 1.3 64.9 + - - +
114B HIS* 4.9 4.3 + - + -
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Residues in contact with ILE 113 (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 CYS* 4.5 7.0 - - + -
36B LEU* 4.0 27.6 - - + -
96B LEU* 2.8 48.3 + - + +
98B LEU* 3.8 22.0 - - + -
111B ARG* 3.4 44.0 - - + +
112B VAL* 1.3 79.0 - - - +
114B HIS* 1.3 69.2 + - - +
118B VAL* 4.2 24.5 - - + -
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Residues in contact with HIS 114 (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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306A ARG 5.5 0.9 - - - -
307A ALA 5.3 7.3 + - - -
340A ILE* 4.8 17.5 - - + -
93B PHE* 4.4 4.0 - - - -
94B VAL 3.5 32.5 - - - +
95B PRO* 3.5 29.8 - - + +
112B VAL* 4.9 2.8 + - + -
113B ILE* 1.3 80.6 - - - +
115B ILE* 1.3 67.5 + - - +
116B ASN* 3.5 14.8 - - - +
117B GLU* 2.9 45.1 + - + +
118B VAL* 3.4 12.6 + - - +
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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