Contacts of the strand formed by residues 132 - 140 (chain A) in PDB entry 4HE2
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 ILE 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.8 31.6 - - + -
73A LEU* 4.7 3.1 - - + -
120A LEU* 4.1 10.5 - - + -
121A ASP 3.3 10.5 - - - +
122A GLY 3.2 28.9 - - - +
125A ASN* 4.2 9.0 - - + -
126A ILE* 3.9 24.7 - - + +
130A ALA 3.7 10.3 - - - +
131A SER* 1.3 79.1 - - - +
133A GLY* 1.3 59.3 + - - +
166A LEU* 3.7 5.7 - - - +
167A TYR* 2.7 42.9 + - + +
247A SER* 3.9 2.7 - - - +
249A VAL* 3.7 7.0 - - - -
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Residues in contact with GLY 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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120A LEU* 3.1 9.9 - - - +
121A ASP* 2.6 43.4 + - - -
132A ILE* 1.3 78.5 - - - +
134A THR* 1.3 60.6 + - - -
165A ALA 3.0 12.6 - - - -
167A TYR* 3.6 8.5 - - - -
249A VAL* 3.6 11.6 - - - +
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Residues in contact with THR 134 (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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37A MET* 3.7 30.7 - - + -
41A ILE* 4.3 6.5 - - + -
44A ILE* 3.9 6.5 - - + +
81A VAL* 4.9 0.2 - - + -
117A PHE* 5.6 0.2 - - + -
118A ASP 3.4 14.4 - - - +
119A PRO* 2.7 24.0 + - + +
133A GLY* 1.3 69.8 - - - -
135A ILE* 1.3 67.0 + - - +
136A PHE* 4.8 1.4 - - + -
164A TYR* 3.1 6.4 - - - +
165A ALA* 2.8 35.4 + - - -
167A TYR* 2.7 31.6 + - - -
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Residues in contact with ILE 135 (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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117A PHE* 3.1 5.6 - - - +
118A ASP* 2.8 41.2 + - + +
121A ASP* 3.6 32.3 - - + +
134A THR* 1.3 81.3 - - - +
136A PHE* 1.3 66.2 + - - +
163A GLY 3.7 7.2 - - - +
164A TYR* 4.5 7.9 - - + -
248A MET* 3.5 30.3 - - + -
249A VAL* 4.8 5.6 - - + -
279A TYR 3.4 18.4 - - - +
280A GLU* 4.1 6.7 - - - +
283A PRO* 3.4 25.6 - - + -
284A VAL* 4.4 8.7 - - + -
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Residues in contact with PHE 136 (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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34A LEU* 4.5 4.9 - - + -
37A MET* 4.0 35.2 - - + -
38A LEU* 5.2 8.1 - - + -
41A ILE* 4.0 21.8 - - + -
115A VAL* 4.5 4.9 - - + -
116A CYS 3.3 9.9 - - - +
117A PHE* 4.0 9.4 - - + -
134A THR 4.8 0.9 - - - -
135A ILE* 1.3 82.3 - - - +
137A ALA* 1.3 60.6 + - - +
138A ILE* 4.1 27.8 - - + -
162A ALA* 3.4 9.2 - - - +
163A GLY* 3.0 64.4 + - - +
164A TYR* 4.0 5.8 - - - -
173A VAL* 5.4 2.5 - - + -
174A ALA 5.0 1.6 - - - -
175A LEU* 4.1 18.8 - - + -
283A PRO* 3.5 8.5 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A VAL 3.8 0.5 - - - +
115A VAL* 3.4 3.3 - - - +
116A CYS* 2.8 35.8 + - + +
136A PHE* 1.3 74.7 - - - +
138A ILE* 1.3 64.0 + - - +
139A TYR* 4.0 20.1 - - + +
159A ILE* 4.1 19.5 - - + -
161A ALA 3.7 5.2 - - - -
162A ALA* 4.0 1.6 - - + -
278A LEU 4.4 5.2 - - - +
283A PRO* 3.8 19.5 - - + +
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Residues in contact with ILE 138 (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 LEU* 4.0 12.3 - - + -
33A LEU* 3.4 30.3 - - + -
34A LEU* 3.7 23.3 - - + -
37A MET* 5.8 0.9 - - + -
113A TYR* 3.8 31.4 - - + -
114A VAL 3.3 7.4 - - - +
115A VAL* 4.1 12.1 - - + -
136A PHE* 4.1 17.3 - - + -
137A ALA* 1.3 78.4 - - - +
139A TYR* 1.3 59.5 + - - +
159A ILE* 3.7 4.3 - - - -
160A VAL* 2.8 33.1 + - + -
161A ALA* 2.8 25.6 + - + +
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Residues in contact with TYR 139 (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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113A TYR* 3.3 12.5 - - - -
114A VAL* 2.8 47.0 + - + +
116A CYS* 4.2 20.6 - - - -
137A ALA* 4.0 21.9 - - + +
138A ILE* 1.3 75.2 - - - +
140A ARG* 1.3 58.5 + - - +
151A ASP 5.2 0.7 - - - -
152A ALA* 5.4 4.5 - - - -
154A GLN* 3.6 42.9 + - + +
155A CYS 3.4 20.4 - - - -
156A GLY* 3.4 14.9 + - - -
158A ASN 3.5 15.3 - - - -
159A ILE* 3.3 31.5 - - + +
160A VAL* 4.2 5.2 - - - -
278A LEU* 5.1 2.3 + - + -
282A ASN* 3.6 15.1 + - - +
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Residues in contact with ARG 140 (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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112A LYS* 3.8 36.8 - - + +
113A TYR* 3.9 15.0 - - + -
114A VAL* 4.7 0.4 - - - -
139A TYR* 1.3 72.5 - - - +
141A LYS* 1.3 79.7 + - - +
142A THR* 3.3 29.7 + - + +
154A GLN* 2.9 22.4 + - - +
158A ASN 4.9 1.0 + - - -
160A VAL* 3.7 15.8 - - + +
401A AMP 5.2 4.5 + - - -
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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