Contacts of the strand formed by residues 124 - 131 (chain B) in PDB entry 6Q3W
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 GLY 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 3.5 2.3 - - - +
68B ARG* 2.8 35.3 + - - -
71B GLY* 4.2 9.5 - - - -
72B LEU 3.5 24.5 - - - -
73B VAL* 4.7 3.8 - - - -
92B LEU* 5.9 0.7 - - - -
123B PRO* 1.3 81.2 - - - +
125B PHE* 1.3 65.6 - - - +
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Residues in contact with PHE 125 (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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63B LEU* 5.4 4.7 - - + -
66B SER 3.2 15.9 - - - +
68B ARG* 3.8 6.0 - - - +
72B LEU 3.1 8.6 + - - +
73B VAL* 3.5 29.9 - - + -
74B SER* 2.9 25.1 + - - +
75B LEU* 3.8 22.7 - - + -
110B VAL* 4.7 5.8 - - + -
114B ILE* 3.9 16.2 - - + -
122B LEU* 5.3 2.2 - - + -
123B PRO 4.1 7.2 - - - -
124B GLY* 1.3 78.5 - - - +
126B SER* 1.3 58.3 + - - +
127B ALA* 3.9 14.8 - - + -
149B THR* 5.4 1.6 - - + -
152B PHE* 3.5 24.2 - + + -
153B LEU* 3.7 22.7 - - + -
156B LEU* 3.6 23.3 - - + -
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Residues in contact with SER 126 (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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20B PHE* 3.5 13.5 - - - -
24B PHE* 3.6 31.0 - - - -
65B GLY* 3.1 2.4 - - - -
66B SER* 2.9 34.0 + - - +
67B PRO 5.9 0.2 - - - -
68B ARG* 4.9 2.4 - - - +
74B SER* 3.4 9.9 - - - -
125B PHE* 1.3 74.1 - - - +
127B ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 127 (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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20B PHE* 3.7 3.5 - - - -
24B PHE* 4.0 3.4 - - - -
63B LEU* 4.6 17.3 - - + -
64B VAL 3.3 11.4 - - - +
65B GLY* 4.4 3.1 - - - -
74B SER 3.0 6.9 + - - +
75B LEU* 3.4 16.3 - - + +
76B LEU 3.1 22.5 + - - -
125B PHE* 3.9 19.7 - - + -
126B SER* 1.3 77.4 - - - +
128B VAL* 1.3 66.0 + - - +
129B VAL* 4.2 1.4 + - + +
152B PHE* 4.7 3.4 - - + -
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Residues in contact with VAL 128 (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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16B ALA* 3.7 32.3 - - - +
19B ALA* 4.1 9.6 - - + -
20B PHE* 3.5 29.6 - - + +
24B PHE* 3.7 16.6 - - + -
62B VAL 3.6 1.9 - - - +
63B LEU* 3.6 3.3 - - - -
64B VAL* 2.8 37.5 + - + +
76B LEU* 3.1 25.4 - - + +
78B THR* 4.7 4.7 - - + -
127B ALA* 1.3 72.1 - - - +
129B VAL* 1.3 64.1 + - - +
130B VAL* 4.1 10.3 + - + -
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Residues in contact with VAL 129 (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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61B THR* 4.1 12.6 - - + -
62B VAL 3.6 2.2 - - - -
63B LEU* 3.7 25.1 - - + -
75B LEU* 5.3 6.7 - - + -
76B LEU 2.7 13.8 + - - +
77B THR* 2.9 41.5 + - - +
78B THR 3.4 4.5 + - - -
79B SER* 5.1 2.0 - - - +
106B TRP* 4.9 14.1 - - + -
110B VAL* 5.0 5.8 - - + -
127B ALA* 5.1 5.4 - - + +
128B VAL* 1.3 75.6 - - - +
130B VAL* 1.3 66.2 + - - +
131B SER* 5.7 0.9 - - - -
145B LEU* 3.7 29.4 - - + -
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Residues in contact with VAL 130 (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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12B LEU* 3.7 31.6 - - + +
15B GLU* 4.2 7.9 - - + +
16B ALA* 3.8 27.6 - - + +
61B THR* 3.3 7.0 - - - +
62B VAL* 2.7 55.6 + - + +
78B THR* 3.6 23.1 - - + +
79B SER* 4.0 5.4 - - - +
128B VAL* 4.1 6.9 + - + -
129B VAL* 1.3 80.8 - - - +
131B SER* 1.3 60.1 + - - +
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Residues in contact with SER 131 (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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12B LEU* 4.0 10.2 - - - +
60B MET 3.2 7.6 + - - -
61B THR* 2.8 28.0 + - - -
79B SER* 3.6 25.7 + - - +
129B VAL* 5.7 1.1 - - - -
130B VAL* 1.3 77.4 - - - +
132B SER* 1.3 61.8 + - - +
133B VAL* 3.1 21.2 + - - +
135B LEU* 4.5 13.6 - - - +
141B SER* 5.2 0.7 - - - -
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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