Contacts of the strand formed by residues 101 - 108 (chain A) in PDB entry 4UAL
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 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 3.6 26.5 - - + -
92A VAL* 3.5 27.8 - - + -
93A VAL 3.4 2.7 - - - +
94A LYS* 3.9 19.7 - - + -
99A GLU 3.5 8.9 + - - +
100A ARG* 1.3 99.6 + - - +
102A TYR* 1.3 65.4 - - - +
155A TYR* 4.1 10.7 + - + +
364A PRO* 3.6 43.3 - - + +
365A SER* 4.1 8.1 - - - +
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.9 21.5 - + - -
92A VAL* 3.6 4.9 - - - +
93A VAL* 2.9 37.6 + - + -
95A MET* 3.9 24.0 - - + +
100A ARG* 3.1 62.4 + - + +
101A ILE* 1.3 76.0 - - - +
103A ALA* 1.3 60.2 + - - +
104A MET 4.1 0.2 - - - -
140A HIS* 4.0 22.2 + + + -
141A TYR* 4.0 18.3 + + - -
152A VAL* 3.4 25.6 - - + -
153A MET 3.2 18.4 - - - +
155A TYR* 3.7 9.2 - - - +
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Residues in contact with ALA 103 (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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82A ILE* 5.0 1.1 - - + -
90A VAL* 4.5 8.1 - - + -
91A ALA 3.4 7.6 - - - +
92A VAL* 4.7 0.2 - - - +
102A TYR* 1.3 73.5 - - - +
104A MET* 1.3 60.4 + - - +
105A LYS 4.2 0.2 - - - -
151A LEU 3.6 1.4 - - - +
152A VAL* 3.5 1.0 - - - -
153A MET* 2.7 42.1 + - + +
154A ASP 3.9 3.8 - - - +
155A TYR* 3.6 10.7 - - + +
501A 3FV 3.3 44.4 - - + +
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Residues in contact with MET 104 (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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73A ARG* 5.2 7.2 - - - +
76A PHE* 3.6 40.6 - - + -
78A ILE* 6.0 3.6 - - - -
89A GLU 3.6 1.6 - - - +
90A VAL* 3.2 3.5 - - - -
91A ALA* 2.8 40.3 + - + +
93A VAL* 3.9 26.7 - - + -
102A TYR 4.1 0.6 - - - -
103A ALA* 1.3 73.8 - - - +
105A LYS* 1.3 64.7 + - - +
106A ILE* 4.0 24.2 + - + +
143A PHE* 4.1 11.9 - - + -
150A TYR* 4.0 18.2 - - + -
151A LEU 3.3 8.3 - - - +
152A VAL* 3.7 20.0 - - + -
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Residues in contact with LYS 105 (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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85A GLY* 5.6 1.4 - - - +
87A PHE 3.5 19.1 + - - -
88A GLY* 4.9 0.2 - - - -
89A GLU 3.3 9.9 - - - +
90A VAL* 4.0 14.8 - - + +
103A ALA 4.2 0.4 + - - -
104A MET* 1.3 74.3 - - - +
106A ILE* 1.3 67.9 + - - +
107A LEU* 3.9 7.7 - - + +
124A GLU* 2.9 26.0 + - - +
149A LEU 3.8 0.3 - - - +
150A TYR* 3.4 5.7 - - - -
151A LEU* 2.9 47.7 + - + +
153A MET* 4.2 11.1 - - + +
218A ASP* 3.7 12.5 + - - -
501A 3FV 3.5 26.8 - - + +
504A EDO 3.1 30.1 + - - -
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Residues in contact with ILE 106 (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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73A ARG* 5.6 6.7 - - + -
78A ILE* 5.9 6.7 - - + -
88A GLY* 3.1 24.6 - - - -
89A GLU* 2.9 38.0 + - + +
91A ALA* 5.8 6.7 - - + -
104A MET* 4.0 22.7 - - + +
105A LYS* 1.3 78.1 - - - +
107A LEU* 1.3 64.2 + - - +
148A HIS* 4.1 20.4 - - + -
149A LEU 3.5 3.8 - - - +
150A TYR* 3.8 30.5 - - + -
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Residues in contact with LEU 107 (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 PHE 3.8 7.9 - - - +
88A GLY* 3.8 24.5 - - - +
105A LYS* 3.9 10.3 - - + +
106A ILE* 1.3 74.8 - - - +
108A ASN* 1.3 59.5 + - - +
111A GLU* 5.9 0.2 - - - +
112A MET* 3.9 28.5 - - + -
121A PHE* 4.5 4.5 - - + -
124A GLU* 4.1 9.0 - - - +
148A HIS* 3.2 11.2 - - - +
149A LEU* 2.8 61.2 + - + +
151A LEU* 4.9 10.1 - - + -
401A PHE* 5.4 1.8 - - + -
504A EDO 3.0 32.1 - - - +
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Residues in contact with ASN 108 (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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107A LEU* 1.3 73.6 - - - +
109A LYS* 1.3 65.6 + - - +
110A TRP* 2.8 29.2 + - - +
111A GLU* 2.9 14.2 + - + +
112A MET* 3.0 26.8 + - - +
147A ASN* 3.6 13.9 + - - +
148A HIS* 4.2 13.8 + - + -
382A ILE* 2.8 53.4 + - + +
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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