Contacts of the strand formed by residues 95 - 101 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ALA* 3.7 20.4 - - + +
58A GLU* 3.8 38.1 - - + +
61A ALA* 4.6 0.7 - - + -
67A LEU* 4.4 2.0 - - - -
68A GLY 3.3 10.1 - - - +
70A ALA 4.3 0.4 - - - +
88A ALA* 4.6 1.6 - - + -
93A THR* 3.3 17.1 + - - +
94A PRO* 1.3 79.9 - - - +
96A LEU* 1.3 69.1 + - - +
97A PHE* 3.5 36.4 + - + -
149A ALA* 4.4 2.2 - - - +
155A GLY 3.8 3.6 + - - +
156A PRO* 3.3 2.8 - - + +
157A VAL* 3.0 26.7 + - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.9 20.9 - - + -
67A LEU* 4.0 10.2 - - + +
68A GLY 2.9 12.3 + - - +
69A VAL* 3.5 11.2 - - + +
70A ALA 2.9 29.3 + - - +
95A VAL* 1.3 72.3 - - - +
97A PHE* 1.3 69.2 + - - +
98A LEU* 3.5 35.8 + - + -
142A VAL* 4.5 4.9 - - + +
145A ALA* 4.3 16.6 - - + +
146A ILE* 3.9 28.5 - - + +
149A ALA* 5.3 1.1 - - + -
157A VAL* 3.8 8.7 - - + +
159A LEU* 4.2 10.8 - - + +
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY* 4.0 17.7 - - - -
58A GLU* 5.1 0.7 - - + -
70A ALA* 3.7 15.9 - - + -
72A VAL* 6.0 4.5 - - + -
81A ALA* 4.3 12.6 - - + -
84A PRO* 3.8 22.7 - - + -
85A ILE* 3.7 46.0 - - + -
88A ALA* 4.6 1.3 - - + -
95A VAL* 3.5 30.5 - - + -
96A LEU* 1.3 74.0 - - - +
98A LEU* 1.3 59.8 + - - +
99A THR* 4.0 0.4 - - - -
156A PRO* 3.7 17.9 - - + -
157A VAL 2.8 20.1 + - - +
158A LEU* 3.4 18.7 - - + +
159A LEU 2.9 28.6 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.0 26.0 - - + -
14A LEU* 4.1 9.6 - - + -
22A LEU* 4.8 6.1 - - + -
33A ILE* 4.9 2.2 - - + -
69A VAL* 3.8 22.4 - - + -
70A ALA 2.7 15.1 + - - +
71A LEU* 3.3 15.8 - - + +
72A VAL* 2.9 27.9 + - - +
96A LEU* 3.5 33.7 - - + -
97A PHE* 1.3 70.5 - - - +
99A THR* 1.3 60.4 + - - +
142A VAL* 4.9 2.9 - - + -
159A LEU* 3.6 24.5 - - + -
161A LEU* 4.3 14.1 - - + -
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.5 2.7 - - - -
72A VAL* 3.2 16.2 + - - +
73A THR 3.6 3.1 + - - -
78A PHE* 3.5 22.4 - - + +
97A PHE 3.9 0.4 + - - -
98A LEU* 1.3 75.9 - - - +
100A GLY* 1.3 77.2 + - - +
118A GLN* 3.9 7.4 - - - +
158A LEU* 3.7 25.6 - - + -
159A LEU 2.8 20.7 + - - +
160A ASP* 3.7 15.7 - - + +
161A LEU* 2.8 37.9 + - - +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 4.6 4.7 - - - -
30A ILE* 3.6 22.0 - - - +
72A VAL 2.7 13.9 + - - -
74A ALA* 3.4 18.9 - - - -
99A THR* 1.3 90.3 + - - +
101A SER* 1.3 58.2 + - - -
118A GLN* 3.1 11.1 - - - +
161A LEU 3.7 7.4 - - - -
166A LEU* 5.1 0.4 - - - -
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.8 3.1 + - - -
74A ALA* 3.4 16.0 - - - +
100A GLY* 1.3 70.8 - - - -
102A GLY* 1.3 63.3 + - - +
103A ALA 3.7 0.2 + - - -
116A ILE 6.1 0.2 - - - -
118A GLN* 3.5 9.4 - - - +
131A ARG* 2.8 27.5 + - - -
160A ASP* 2.7 37.2 + - - -
161A LEU 3.6 4.9 + - - -
162A PRO* 3.5 6.1 - - - +
163A TRP* 3.1 21.5 + - - +
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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