Contacts of the strand formed by residues 95 - 101 (chain B) in PDB entry 2HEI
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 ALA 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 5.9 0.2 - - + -
22B LYS 3.3 5.3 + - - +
23B LEU* 3.2 19.7 - - + -
24B VAL* 3.1 18.7 + - - -
71B PHE* 4.9 1.1 - - + -
93B ALA* 4.1 3.8 - - - +
94B GLN* 1.3 82.2 - - + +
96B ALA* 1.3 62.4 + - - +
126B ILE* 3.6 9.4 - - - +
127B VAL* 3.1 14.8 - - + +
177B ILE* 3.8 26.2 - - + -
181B LEU* 4.5 8.5 - - + -
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Residues in contact with ALA 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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23B LEU* 4.4 1.1 - - - -
24B VAL* 3.1 18.8 - - + +
26B LEU* 4.8 3.1 - - + -
95B ALA* 1.3 77.0 - - - +
97B ILE* 1.3 66.7 + - - +
98B VAL 4.2 0.2 - - - -
118B LEU* 3.8 39.9 - - + -
126B ILE* 3.9 6.3 - - + +
127B VAL 2.9 7.7 + - - +
128B ILE* 3.4 4.3 - - + +
129B ALA* 2.9 25.3 + - - +
177B ILE* 5.0 1.3 - - - +
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Residues in contact with ILE 97 (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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23B LEU* 4.0 10.3 - - + -
24B VAL 2.9 5.7 + - - -
25B LEU* 3.4 15.8 - - + +
26B LEU* 2.8 27.0 + - - +
36B LEU* 5.5 1.1 - - + -
96B ALA* 1.3 74.4 - - - +
98B VAL* 1.3 61.7 + - - +
99B VAL* 3.8 20.3 - - + +
129B ALA* 3.3 9.9 - - + +
131B ALA* 4.0 19.3 - - + +
173B LEU* 4.1 15.0 - - + -
174B PHE* 3.7 32.8 - - + -
177B ILE* 3.5 33.9 - - + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.4 16.2 - - + +
27B GLY* 4.8 0.9 - - - +
97B ILE* 1.3 73.8 - - - +
99B VAL* 1.3 63.8 + - - +
111B ALA* 3.5 40.8 - - + +
114B TRP* 4.0 11.0 - - + -
115B VAL* 3.9 20.6 - - + +
118B LEU* 3.6 30.7 - - + -
128B ILE* 4.3 2.0 - - + -
129B ALA 2.9 14.3 + - - +
130B LEU* 3.4 11.9 - - + +
131B ALA 2.9 22.6 + - - -
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Residues in contact with VAL 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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25B LEU* 4.3 7.0 - - + -
26B LEU 2.8 15.5 + - - +
27B GLY* 3.4 19.2 - - - -
28B GLU 4.2 0.7 + - - -
31B VAL* 3.6 28.2 - - + +
33B LYS* 4.2 12.3 - - + +
36B LEU* 3.8 24.7 - - + -
97B ILE* 3.8 17.5 - - + +
98B VAL* 1.3 81.0 - - - +
100B TYR* 1.3 75.2 + - - +
107B THR 4.7 1.2 - - - +
111B ALA* 4.5 2.6 - - - +
131B ALA* 3.4 9.0 - - + +
133B ASN* 3.7 17.5 - - + -
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Residues in contact with TYR 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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31B VAL* 4.0 10.3 - - - -
99B VAL* 1.3 73.7 - - - +
101B ASP* 1.3 66.7 + - - +
102B ILE* 4.0 11.5 - - + +
107B THR* 3.4 27.8 - - - +
108B PHE* 3.7 28.9 - + + +
111B ALA* 4.1 3.1 - - + -
130B LEU* 4.0 28.5 - - + -
131B ALA 3.0 14.3 + - - +
132B GLY* 3.3 25.5 - - - -
133B ASN* 2.8 34.5 + - - +
143B VAL* 3.5 26.1 - - + +
145B TYR* 5.4 0.2 - - - -
148B ALA* 3.2 21.3 - - - +
159B PHE* 3.3 13.5 - + - -
161B GLU* 4.4 2.9 + - - -
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Residues in contact with ASP 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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30B ALA 4.7 1.4 - - - +
31B VAL* 3.9 19.9 - - + +
100B TYR* 1.3 76.4 - - - +
102B ILE* 1.3 59.3 + - - +
103B THR* 2.6 37.4 + - - +
104B ASN* 3.0 26.7 + - - +
107B THR* 2.9 27.6 + - + +
133B ASN 3.5 5.6 - - - -
134B LYS* 3.6 31.7 + - - +
143B VAL* 4.0 0.3 - - - +
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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