Contacts of the strand formed by residues 118 - 124 (chain A) in PDB entry 4UJ3
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL 2.9 7.5 + - - +
86A GLY* 3.1 0.7 - - - -
87A ALA 2.7 32.7 + - - +
116A ASN 4.2 7.0 - - - +
117A ILE* 1.3 70.6 - - - +
119A ILE* 1.3 59.1 + - - +
149A SER* 5.1 0.4 - - - +
168A ILE* 3.7 20.1 - - + +
171A GLU* 3.3 36.6 - - + +
172A ILE* 3.2 40.6 - - + +
175A ILE* 4.4 13.0 - - + -
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Residues in contact with ILE 119 (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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87A ALA* 3.6 9.0 - - + +
89A LEU* 4.6 8.5 - - + -
106A LEU* 3.9 17.3 - - + -
109A LEU* 3.5 41.1 - - + -
117A ILE* 3.4 26.5 + - + +
118A VAL* 1.3 78.7 - - - +
120A MET* 1.3 68.7 + - - +
147A GLY 4.5 2.7 + - - +
148A LEU* 3.3 34.6 - - + -
149A SER* 3.3 21.3 + - - -
171A GLU* 5.3 0.2 - - - +
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Residues in contact with MET 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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87A ALA 2.9 8.9 + - - +
88A LEU* 3.2 36.3 - - + -
89A LEU* 2.8 32.2 + - - +
118A VAL 4.1 0.2 + - - -
119A ILE* 1.3 77.2 - - - +
121A LEU* 1.3 68.0 + - - +
122A VAL* 3.7 10.7 + - + +
149A SER* 3.0 31.4 - - - +
150A PHE 4.9 0.9 - - - -
151A ILE* 3.8 12.6 - - + -
164A ALA* 3.1 46.2 - - + +
167A THR* 4.2 15.5 - - - -
168A ILE* 4.1 10.5 - - + +
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Residues in contact with LEU 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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89A LEU* 3.5 20.9 - - + +
91A TYR* 4.0 14.8 - - + -
99A TYR* 4.5 12.6 - - + -
102A VAL* 3.7 35.2 - - + -
119A ILE 4.2 0.4 - - - -
120A MET* 1.3 74.6 - - - +
122A VAL* 1.3 61.4 + - - +
123A GLY 4.2 0.2 - - - -
139A ALA 4.2 8.7 - - - +
142A PHE* 4.1 26.2 - - + -
143A ALA* 4.2 5.4 - - + -
148A LEU* 4.5 12.9 - - + +
149A SER 2.7 16.0 + - - +
150A PHE* 3.2 21.1 - - + -
151A ILE 3.2 23.0 + - - +
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Residues in contact with VAL 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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27A LEU* 4.5 12.1 - - + -
88A LEU* 4.1 16.4 - - + -
89A LEU 2.9 11.8 + - - +
90A VAL* 3.5 10.3 - - + +
91A TYR* 3.0 32.1 + - - +
120A MET* 3.7 34.3 - - + +
121A LEU* 1.3 79.1 - - - +
123A GLY* 1.3 63.0 + - - +
124A ASN* 3.6 1.4 + - + +
151A ILE* 3.4 5.2 - - + +
153A THR* 3.3 42.6 - - + +
164A ALA* 5.1 1.8 - - + -
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Residues in contact with GLY 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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91A TYR* 3.3 19.8 + - - -
93A ILE* 2.9 27.2 - - - +
121A LEU 4.2 0.2 - - - -
122A VAL* 1.3 71.8 - - - +
124A ASN* 1.3 52.7 + - - -
126A SER* 4.8 0.2 - - - -
150A PHE* 4.4 1.2 - - - -
151A ILE 3.0 11.2 + - - -
152A GLU* 3.1 9.0 - - - +
153A THR 2.6 32.9 + - - +
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Residues in contact with ASN 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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22A VAL 2.9 27.3 + - - +
23A GLY* 3.7 11.1 + - - -
27A LEU* 3.8 10.1 - - + +
90A VAL* 4.0 11.0 - - + -
91A TYR 3.0 13.0 + - - +
92A ASP* 3.8 0.2 - - - +
93A ILE* 3.2 21.0 + - - +
122A VAL* 3.6 0.4 + - + -
123A GLY* 1.3 72.9 - - - +
125A LYS* 1.3 83.1 + - - +
126A SER 3.3 2.0 - - - -
153A THR* 2.9 24.6 + - - +
155A ALA* 3.3 15.5 + - - +
200A GNP 3.3 23.8 + - - -
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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