Contacts of the strand formed by residues 117 - 124 (chain A) in PDB entry 2H4J
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 GLY 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ASN 3.9 3.1 - - - +
100A ILE* 3.8 11.9 - - - -
114A GLU* 3.7 24.1 + - - +
115A LEU 3.6 2.6 + - - -
116A HIS* 1.3 80.0 + - - +
118A ASN* 1.3 69.3 + - - +
158A ASN* 3.3 16.6 - - - -
159A ILE* 4.3 0.9 - - - -
160A VAL* 4.1 5.1 - - - +
167A PRO* 5.2 3.0 - - - +
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Residues in contact with ASN 118 (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 ILE* 3.4 13.7 - - - +
102A ARG* 3.4 35.2 + - + +
114A GLU* 3.9 6.9 + - - +
116A HIS 4.0 0.6 + - - -
117A GLY* 1.3 79.4 - - - +
119A VAL* 1.3 60.3 + - - +
120A GLU* 3.0 27.7 + - - +
121A GLU* 3.0 46.4 + - - +
157A PRO* 5.2 0.3 - - - +
158A ASN* 2.9 27.6 + - - +
159A ILE* 3.4 14.1 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.7 25.4 - - + +
71A MET* 3.5 20.9 - - + -
72A LEU* 4.1 20.6 - - + +
100A ILE* 2.9 47.3 + - + +
101A ASP* 4.2 14.8 - - - +
102A ARG* 4.8 0.4 - - + -
106A ARG* 4.8 2.0 - - - +
118A ASN* 1.3 72.3 - - - +
120A GLU* 1.3 66.2 + - + +
121A GLU 3.7 0.4 - - - -
122A TYR* 3.9 8.8 + - - -
133A VAL* 3.5 22.7 - - + +
159A ILE* 4.5 5.6 - - + -
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Residues in contact with GLU 120 (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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72A LEU* 4.3 11.3 - - + +
102A ARG* 2.9 40.6 + - + +
106A ARG* 3.1 25.6 + - - -
118A ASN* 3.0 7.3 + - - +
119A VAL* 1.3 90.7 - - + +
121A GLU* 1.3 60.5 + - + +
132A THR* 3.6 5.9 - - - -
133A VAL* 2.8 38.2 + - + +
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Residues in contact with GLU 121 (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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102A ARG* 3.4 21.8 + - - +
118A ASN* 3.0 24.1 + - - +
120A GLU* 1.3 78.0 - - + +
122A TYR* 1.3 67.1 + - - +
131A TYR 3.9 3.8 - - - +
132A THR* 5.0 0.2 - - - +
157A PRO* 3.8 0.5 - - - +
158A ASN* 2.9 59.4 + - + +
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Residues in contact with TYR 122 (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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60A PHE* 4.7 3.6 - - - -
61A TYR* 3.3 32.8 - + - -
68A ILE* 4.6 8.8 - - - +
69A PHE* 3.5 21.6 - + - -
119A VAL 3.9 11.3 + - - -
121A GLU* 1.3 82.1 - - - +
123A TYR* 1.3 67.9 + - - +
130A LYS* 3.5 5.5 - - - +
131A TYR* 2.8 39.1 + - + +
133A VAL* 3.7 40.1 - - + +
136A VAL* 3.6 19.3 - - + -
155A ILE* 3.7 11.7 - - + -
156A ARG 3.3 22.4 - - - -
157A PRO* 3.5 20.5 - - + +
158A ASN 4.3 0.7 - - - +
159A ILE* 5.4 0.9 - - + +
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Residues in contact with TYR 123 (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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122A TYR* 1.3 80.3 - - - +
124A CYS* 1.3 76.7 + - - +
125A VAL* 3.3 7.0 + - - -
128A GLU* 4.1 27.8 - - + +
129A LYS 3.3 12.6 - - - +
130A LYS* 4.5 3.8 - - + -
131A TYR 4.5 0.4 - - - +
155A ILE* 4.0 5.1 - - - +
156A ARG* 2.8 77.4 + - + +
157A PRO 4.2 0.4 - - - -
158A ASN* 3.8 41.3 + - + -
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Residues in contact with CYS 124 (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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123A TYR* 1.3 75.1 - - - +
125A VAL* 1.3 61.0 + - - +
126A ARG 3.4 15.3 - - - -
127A CYS* 3.5 9.6 - - - -
128A GLU* 2.9 27.2 + - - +
129A LYS 3.0 14.3 + - - +
131A TYR* 4.8 0.2 - - + -
148A CYS* 3.6 20.0 - - + -
151A CYS* 3.5 9.2 - - - -
153A SER* 3.6 10.3 - - - -
154A LEU 3.6 5.2 - - - -
155A ILE* 4.1 8.7 - - + +
1001A ZN 2.4 36.3 - - - -
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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