Contacts of the strand formed by residues 112 - 121 (chain A) in PDB entry 3UR9
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 ARG 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A THR* 4.6 6.7 - - - +
30A HIS* 3.4 29.8 - - - +
54A GLU* 2.7 35.3 + - + +
108A ARG* 3.4 2.8 - - - -
109A ILE 2.9 31.6 + - - +
110A GLN 3.9 6.5 - - - +
111A GLY* 1.3 81.2 - - - +
113A LEU* 1.3 61.9 + - - +
114A VAL* 3.3 3.9 + - + +
203A K36 3.5 29.7 - - + +
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Residues in contact with LEU 113 (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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53A GLY* 3.4 26.5 - - - +
54A GLU* 3.8 7.1 + - - +
106A SER* 4.3 16.8 - - - +
107A MET 3.3 26.9 - - - +
108A ARG* 4.7 4.4 - - + +
111A GLY 3.9 2.2 + - - -
112A ARG* 1.3 70.2 - - - +
114A VAL* 1.3 62.0 + - - +
115A HIS* 4.8 2.0 - - + +
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Residues in contact with VAL 114 (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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53A GLY 3.5 7.4 - - - +
54A GLU* 3.9 20.2 - - + -
105A ALA 3.5 0.7 - - - +
106A SER* 4.5 0.9 - - - -
107A MET* 2.7 41.8 + - + +
109A ILE* 4.0 27.1 - - + -
112A ARG 3.8 10.5 - - - +
113A LEU* 1.3 75.6 - - - +
115A HIS* 1.3 69.4 + - - +
116A GLY* 3.3 8.1 + - - +
158A ALA* 4.5 6.1 - - + -
168A VAL* 4.1 22.2 - - + -
170A ALA* 4.3 8.7 - - + -
203A K36 4.3 10.1 - - + -
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 5.2 0.7 - - - +
53A GLY* 3.0 25.3 + - - +
75A GLU* 2.9 27.4 + - - -
104A ILE* 4.0 17.7 - - + +
105A ALA* 3.8 7.0 + - - -
106A SER* 3.2 24.0 + - - +
113A LEU* 4.0 2.8 - - + +
114A VAL* 1.3 71.4 - - - +
116A GLY* 1.3 56.9 + - - +
170A ALA* 3.4 4.9 - - - -
171A VAL* 2.8 56.3 + - + +
173A ALA* 4.1 13.9 - - - -
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Residues in contact with GLY 116 (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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104A ILE* 3.2 7.3 - - - +
105A ALA 2.8 39.3 + - - -
107A MET* 3.7 13.0 - - - +
114A VAL* 3.3 5.0 + - - -
115A HIS* 1.3 77.6 - - - +
117A GLN* 1.3 59.3 + - - -
169A CYS 2.9 15.5 - - - -
170A ALA* 4.1 0.9 - - - -
171A VAL* 4.0 8.3 - - - -
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Residues in contact with GLN 117 (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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76A GLY* 3.2 9.7 - - - -
77A CYS* 2.9 47.5 + - - -
78A PRO 4.4 2.4 + - - -
79A GLU* 4.4 1.0 - - - +
101A MET* 3.7 32.3 - - + +
102A GLY 2.8 28.9 + - - +
103A ALA 3.5 6.3 - - - +
104A ILE* 3.5 16.0 - - + +
107A MET* 4.1 1.0 - - - +
116A GLY* 1.3 76.0 - - - +
118A SER* 1.3 63.5 + - - +
154A CYS* 5.2 0.5 - - - -
168A VAL* 3.3 4.5 - - - -
169A CYS* 2.8 40.4 + - - -
171A VAL* 4.2 3.5 - - + +
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Residues in contact with SER 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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101A MET* 3.5 7.6 - - - +
102A GLY* 2.7 31.1 + - - -
103A ALA* 3.3 22.0 + - - +
107A MET* 4.9 9.0 - - - +
116A GLY 4.4 0.2 - - - -
117A GLN* 1.3 77.0 - - - +
119A GLY* 1.3 53.4 + - - +
166A THR* 4.2 14.4 - - - -
167A VAL 3.2 10.1 - - - -
168A VAL* 4.2 10.7 - - - +
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Residues in contact with GLY 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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99A VAL* 3.6 16.6 - - - -
100A ARG 3.2 12.8 - - - -
101A MET* 3.9 4.0 - - - +
102A GLY* 4.0 1.6 - - - -
118A SER* 1.3 76.4 - - - +
120A MET* 1.3 60.5 + - - -
166A THR* 3.3 8.3 - - - +
167A VAL* 2.8 34.0 + - - +
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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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99A VAL* 3.4 3.0 - - - -
100A ARG* 2.9 48.8 + - + +
119A GLY* 1.3 73.4 - - - -
121A LEU* 1.3 74.1 + - - +
122A LEU* 3.4 21.8 + - + +
165A ASN 3.6 20.0 - - - +
166A THR* 4.6 4.5 - - - +
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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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85A VAL* 5.6 0.4 - - + -
97A LEU* 4.1 26.2 - - + -
98A ALA 3.7 3.4 - - - +
99A VAL* 3.5 25.5 - - + +
119A GLY 4.1 0.6 + - - -
120A MET* 1.3 83.0 - - - +
122A LEU* 1.3 66.4 + - - +
133A GLY* 4.1 24.9 - - - +
134A THR* 4.7 1.6 - - + +
165A ASN* 2.9 48.4 + - + +
167A VAL* 3.8 19.5 - - + -
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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