Contacts of the strand formed by residues 95 - 101 (chain B) in PDB entry 2AG1
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 VAL 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ALA* 3.6 23.3 - - + +
58B GLU* 3.8 36.6 - - + +
61B ALA* 4.6 0.4 - - + -
67B LEU* 4.5 1.8 - - - -
68B GLY 3.2 9.4 - - - +
70B ALA 4.3 0.4 - - - +
88B ALA* 4.6 1.3 - - + -
93B THR* 3.2 17.1 + - - +
94B PRO* 1.3 78.8 - - - +
96B LEU* 1.3 68.6 + - - +
97B PHE* 3.5 32.9 + - + -
149B ALA* 4.4 2.1 - - - +
155B GLY 3.8 3.0 + - - +
156B PRO* 3.3 3.3 - - + +
157B VAL* 3.1 26.0 + - - +
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Residues in contact with LEU 96 (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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14B LEU* 3.9 21.5 - - + -
67B LEU* 4.0 10.3 - - + +
68B GLY 2.8 13.3 + - - +
69B VAL* 3.5 12.6 - - + +
70B ALA 2.9 28.2 + - - +
95B VAL* 1.3 70.8 - - - +
97B PHE* 1.3 69.7 + - - +
98B LEU* 3.6 34.9 + - + -
142B VAL* 4.4 5.6 - - + +
145B ALA* 4.2 17.3 - - + +
146B ILE* 3.9 30.1 - - + +
149B ALA* 5.3 1.3 - - + -
157B VAL* 3.8 8.7 - - + +
159B LEU* 4.2 11.7 - - + +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 3.9 9.6 - - - -
58B GLU* 5.1 0.4 - - + -
70B ALA* 3.6 24.2 - - + -
72B VAL* 6.0 4.3 - - + -
81B ALA* 4.3 13.0 - - + -
84B PRO* 3.8 22.7 - - + -
85B ILE* 3.7 46.2 - - + -
88B ALA* 4.6 1.6 - - + -
95B VAL* 3.5 31.0 - - + -
96B LEU* 1.3 73.8 - - - +
98B LEU* 1.3 61.0 + - - +
99B THR 3.9 0.8 + - - -
156B PRO* 3.8 18.2 - - + -
157B VAL 2.8 20.5 + - - +
158B LEU* 3.5 19.2 - - + +
159B LEU 2.9 26.9 + - - +
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Residues in contact with LEU 98 (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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10B VAL* 4.1 24.2 - - + -
14B LEU* 4.1 9.2 - - + -
22B LEU* 4.8 6.5 - - + -
33B ILE* 4.9 3.1 - - + -
69B VAL* 3.8 22.0 - - + -
70B ALA 2.8 15.6 + - - +
71B LEU* 3.3 15.4 - - + +
72B VAL* 2.8 29.0 + - - +
96B LEU* 3.7 32.5 - - + -
97B PHE* 1.3 73.4 - - - +
99B THR* 1.3 59.3 + - - +
142B VAL* 4.9 2.9 - - + -
159B LEU* 3.6 20.9 - - + -
161B LEU* 4.1 18.4 - - + -
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Residues in contact with THR 99 (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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30B ILE* 4.6 2.2 - - - -
72B VAL* 3.2 19.0 + - - +
73B THR 3.7 1.6 + - - -
78B PHE* 3.5 22.6 - - + +
97B PHE 3.9 0.2 + - - -
98B LEU* 1.3 74.6 - - - +
100B GLY* 1.3 74.1 + - - +
118B GLN* 3.9 8.7 - - - +
158B LEU* 3.7 25.4 - - + -
159B LEU 2.9 18.6 + - - +
160B ASP* 3.6 14.8 - - + +
161B LEU* 2.8 33.4 + - - +
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Residues in contact with GLY 100 (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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29B HIS* 4.8 4.5 - - - -
30B ILE* 3.7 19.2 - - - +
72B VAL 2.8 14.3 + - - -
74B ALA* 3.2 18.9 - - - -
99B THR* 1.3 88.0 + - - +
101B SER* 1.3 60.0 + - - -
118B GLN* 2.9 11.6 - - - +
161B LEU 3.5 9.9 - - - -
166B LEU* 5.1 0.4 - - - -
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Residues in contact with SER 101 (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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29B HIS* 3.8 3.6 + - - -
74B ALA* 3.3 15.0 - - - +
100B GLY* 1.3 74.3 - - - -
102B GLY* 1.3 65.1 + - - +
103B ALA 3.7 0.2 + - - -
116B ILE 6.1 0.2 - - - -
118B GLN* 3.5 9.9 - - - +
131B ARG* 2.9 22.4 + - - -
160B ASP* 2.6 34.6 + - - -
161B LEU 3.5 4.9 + - - -
162B PRO* 3.4 7.4 - - - +
163B TRP* 3.0 22.0 + - - +
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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