Contacts of the strand formed by residues 124 - 131 (chain D) in PDB entry 6GR2
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D PRO* 3.4 4.0 - - - +
68D ARG* 2.7 35.8 + - - +
71D GLY* 4.2 6.2 - - - -
72D LEU 2.9 26.7 - - - -
73D VAL* 4.7 0.2 - - - -
92D LEU* 3.3 13.7 - - - +
123D PRO* 1.3 81.2 - - - +
125D PHE* 1.3 59.3 + - - +
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Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 5.9 2.0 - - + -
66D SER 3.1 18.2 - - - +
67D PRO* 4.1 0.4 - - + -
68D ARG* 3.3 11.8 - - - +
72D LEU 2.8 4.9 + - - -
73D VAL* 3.3 38.7 - - + -
74D SER 2.9 24.6 + - - -
75D LEU* 3.8 13.9 - - + -
92D LEU* 5.3 0.4 - - + -
110D VAL* 5.3 1.6 - - + -
114D ILE* 3.7 18.4 - - + -
122D LEU* 5.2 2.5 - - + -
123D PRO 3.5 10.8 - - - -
124D GLY* 1.3 75.1 - - - +
126D SER* 1.3 59.2 + - - +
127D ALA* 4.0 11.7 - - + -
149D THR* 5.7 2.9 - - + -
152D PHE* 3.4 26.7 - + + -
153D LEU* 3.8 25.1 - - + -
156D LEU* 3.4 22.0 - - + -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 4.0 7.6 - - - -
24D PHE* 3.5 32.6 - - - -
65D GLY* 2.8 3.1 - - - -
66D SER* 2.8 35.8 + - - +
68D ARG* 2.8 35.9 + - - +
74D SER* 3.2 5.7 - - - -
125D PHE* 1.3 73.8 - - - +
127D ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 4.3 1.3 - - - -
24D PHE* 4.1 3.2 - - - -
63D LEU* 3.5 24.9 - - + -
64D VAL 3.0 13.5 - - - +
65D GLY* 3.8 1.6 - - - -
74D SER 3.0 5.9 + - - +
75D LEU* 3.4 12.5 - - + +
76D LEU 3.0 22.7 + - - -
125D PHE* 4.0 19.7 - - + -
126D SER* 1.3 77.1 - - - +
128D VAL* 1.3 64.8 + - - +
129D VAL* 5.4 2.2 - - + +
152D PHE* 4.4 0.4 - - + -
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 3.1 35.0 - - + +
19D ALA* 4.6 5.6 - - + -
20D PHE* 3.6 30.7 - - + +
24D PHE* 3.9 10.8 - - + -
62D VAL 3.8 1.0 - - - +
63D LEU* 3.5 5.2 - - - +
64D VAL* 2.8 39.6 + - + -
76D LEU* 2.9 27.8 - - + +
78D THR* 5.4 0.7 - - + -
127D ALA* 1.3 79.0 - - - +
129D VAL* 1.3 63.4 + - - +
130D VAL* 4.2 1.5 + - + -
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D THR* 3.6 28.9 - - + -
62D VAL 3.6 3.8 - - - +
63D LEU* 4.1 21.3 - - + -
75D LEU* 6.0 5.6 - - + -
76D LEU 2.6 15.8 + - - +
77D THR* 3.3 16.5 + - - +
78D THR* 3.0 27.2 + - - +
106D TRP* 5.4 7.4 - - + -
110D VAL* 6.2 1.8 - - + -
127D ALA* 5.4 3.4 - - + +
128D VAL* 1.3 78.5 - - - +
130D VAL* 1.3 69.5 + - - +
131D SER* 5.2 2.9 - - - -
145D LEU* 3.8 21.8 - - + -
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.7 26.4 - - + +
15D GLU* 4.4 8.3 - - + -
16D ALA* 3.6 41.5 - - + +
61D THR* 3.5 2.4 - - - +
62D VAL* 2.8 46.3 + - + +
78D THR* 3.2 32.8 - - + +
79D SER* 4.9 1.6 - - - -
128D VAL* 5.0 1.3 - - + -
129D VAL* 1.3 77.7 - - - +
131D SER* 1.3 64.6 + - - +
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.8 6.4 - - - +
60D MET 3.2 5.6 + - - -
61D THR* 3.2 24.7 + - - -
78D THR* 4.9 0.8 + - - -
79D SER* 4.1 20.1 + - - -
129D VAL* 5.2 2.9 - - - -
130D VAL* 1.3 78.2 - - - +
132D SER* 1.3 58.1 + - - +
133D VAL* 3.1 29.2 + - - +
135D LEU* 4.7 6.3 - - - +
141D SER* 5.1 1.2 - - - -
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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