Contacts of the strand formed by residues 127 - 133 (chain A) 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 VAL 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLN 3.0 12.0 + - - +
95A ALA* 3.2 5.9 - - + +
96A ALA 2.9 26.0 + - - +
125A SER 4.2 6.7 - - - +
126A ILE* 1.4 73.0 - - - +
128A ILE* 1.3 62.4 + - - +
129A ALA 4.2 0.2 + - - -
158A LEU* 4.1 19.3 - - + -
177A ILE* 4.2 11.6 - - + +
180A LYS* 4.0 38.8 - - + +
181A LEU* 3.8 24.7 - - + -
182A PRO* 5.8 0.7 - - + -
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Residues in contact with ILE 128 (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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96A ALA* 3.4 5.6 - - + +
98A VAL* 4.4 6.5 - - + -
115A VAL* 4.7 8.7 - - + +
118A LEU* 3.8 44.9 - - + -
119A GLN* 4.4 17.7 - - + +
126A ILE* 3.7 24.8 + - + +
127A VAL* 1.3 79.2 - - - +
129A ALA* 1.3 70.6 + - - +
156A SER 4.5 3.5 + - - +
157A LEU* 3.5 32.8 - - + -
158A LEU* 3.1 22.9 + - - +
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Residues in contact with ALA 129 (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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96A ALA 2.8 8.7 + - - +
97A ILE* 3.3 7.1 - - + -
98A VAL* 2.8 27.1 + - - +
127A VAL 4.2 0.2 + - - -
128A ILE* 1.3 81.4 - - - +
130A LEU* 1.3 60.6 + - - +
157A LEU* 5.0 0.4 - - - -
158A LEU* 3.4 20.4 - - + -
173A LEU* 4.0 13.5 - - + -
177A ILE* 3.8 30.1 - - + -
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Residues in contact with LEU 130 (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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98A VAL* 3.3 20.9 - - + +
100A TYR* 3.9 27.6 - - + -
108A PHE* 4.2 6.7 - - + -
111A ALA* 4.1 18.8 - - + -
115A VAL* 4.7 9.9 - - + -
129A ALA* 1.3 75.1 - - - +
131A ALA* 1.4 59.1 + - - +
132A GLY 4.2 0.2 - - - -
148A ALA 4.2 9.0 - - - +
151A TYR* 3.8 28.0 - - + -
152A ALA* 4.5 3.8 - - + -
157A LEU* 4.3 10.5 - - + +
158A LEU 2.8 14.2 + - - +
159A PHE* 3.3 22.5 - - + -
160A MET 3.2 23.6 + - - -
173A LEU* 4.7 2.3 - - - +
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Residues in contact with ALA 131 (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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36A LEU* 4.6 3.8 - - + -
97A ILE* 3.9 13.0 - - + -
98A VAL 2.9 10.0 + - - +
99A VAL* 3.4 11.3 - - + +
100A TYR* 2.9 30.4 + - - +
129A ALA 4.2 0.2 - - - -
130A LEU* 1.4 73.4 - - - +
132A GLY* 1.3 59.4 + - - +
133A ASN 3.4 2.6 + - - -
160A MET 3.3 5.2 - - - +
162A THR* 4.1 14.6 - - + +
173A LEU* 3.6 24.7 - - + -
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Residues in contact with GLY 132 (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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100A TYR* 3.3 33.5 - - - -
102A ILE* 3.5 10.2 - - - +
131A ALA* 1.3 68.3 - - - +
133A ASN* 1.3 61.8 + - - -
135A ALA* 4.1 0.7 - - - +
159A PHE* 4.1 2.0 - - - -
160A MET 3.0 12.2 + - - -
161A GLU* 3.2 11.7 - - - +
162A THR 2.8 23.9 + - - +
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Residues in contact with ASN 133 (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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31A VAL 2.9 23.5 + - - +
32A GLY* 3.6 9.5 + - - -
36A LEU* 3.6 10.3 - - - +
99A VAL* 3.8 11.9 - - + -
100A TYR 2.9 18.5 + - - +
101A ASP* 3.6 0.2 - - - -
102A ILE* 3.0 22.3 + - - +
131A ALA 3.4 0.4 + - - -
132A GLY* 1.3 72.3 - - - +
134A LYS* 1.3 80.2 + - - +
135A ALA 3.2 2.7 + - - -
162A THR* 2.8 28.3 + - - +
164A ALA 3.3 16.3 + - - -
201A GDP 3.2 26.2 + - - -
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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