Contacts of the strand formed by residues 94 - 109 (chain B) 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 LEU 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PRO* 3.6 44.9 - - + +
4A THR* 4.3 6.1 - - - +
7A SER* 3.7 12.4 + - - -
67A ASP* 5.0 0.6 + - - -
201A CL 4.1 17.9 - - + -
6B TRP* 3.8 33.0 - - + -
87B ILE 3.7 2.2 - - - -
88B LYS* 3.8 26.7 - - + -
92B GLY 3.4 11.4 + - - +
93B GLU* 1.3 83.6 - - - +
95B LEU* 1.3 61.5 + - - +
96B PRO* 3.7 7.9 - - + +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TRP* 4.0 0.4 - - - -
85B VAL 3.5 0.7 - - - +
87B ILE* 2.8 39.2 + - + +
89B ARG* 3.6 39.0 - - + +
93B GLU* 3.9 22.7 - - + +
94B LEU* 1.3 75.4 - - - +
96B PRO* 1.3 68.1 - - + +
97B LEU* 3.2 29.8 + - + +
132B LEU* 4.0 31.4 - - + -
133B GLY 4.0 7.6 - - - +
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Residues in contact with PRO 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B MET* 6.5 0.7 - - - -
1B ALA* 6.2 0.4 - - + -
6B TRP* 3.8 25.3 - - + -
84B SER* 3.5 16.6 - - - +
85B VAL 3.3 8.7 - - - +
86B LEU* 4.4 1.3 - - + -
94B LEU* 3.7 8.5 - - + +
95B LEU* 1.3 88.0 - - + +
97B LEU* 1.3 65.2 + - - +
98B ALA 4.1 1.0 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B SER* 3.4 4.0 - - - -
85B VAL* 2.8 42.4 + - + +
87B ILE* 3.1 33.0 - - + -
95B LEU* 3.7 26.5 - - + +
96B PRO* 1.3 76.6 - - - +
98B ALA* 1.3 62.9 + - - +
99B VAL 3.7 0.7 + - - -
121B LEU* 4.0 22.2 - - + -
132B LEU* 3.9 25.6 - - + +
133B GLY* 4.0 13.7 - - - +
134B THR* 3.6 18.8 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B VAL* 4.5 6.3 - - + -
83B CYS 3.4 8.5 - - - +
84B SER* 4.6 2.0 - - - +
96B PRO 4.1 2.2 + - - -
97B LEU* 1.3 72.0 - - - +
99B VAL* 1.3 60.9 + - - +
121B LEU* 3.6 6.2 - - - +
122B LEU* 2.9 47.7 + - + -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.4 1.6 - - - -
83B CYS* 2.9 46.7 + - + +
85B VAL* 3.9 21.3 - - + -
98B ALA* 1.3 76.2 - - - +
100B ARG* 1.3 63.2 + - - +
101B MET* 3.6 18.5 + - - -
119B GLY* 3.6 28.9 - - - -
120B MET 3.4 15.0 - - - +
121B LEU* 4.1 9.2 - - + +
122B LEU* 3.9 5.3 - - - +
143B TYR* 4.3 1.1 - - + -
167B VAL* 3.7 13.9 - - + -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLY* 4.0 26.7 - - - +
81B THR 3.7 3.4 - - - -
82B VAL* 4.5 9.9 - - + +
99B VAL* 1.3 70.8 - - - +
101B MET* 1.3 64.8 + - - +
102B GLY* 4.8 0.2 - - - -
119B GLY* 4.2 0.4 - - - -
120B MET* 2.9 41.4 + - + +
122B LEU* 3.9 26.8 - - + +
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B CYS* 3.5 27.1 - - - -
78B PRO 4.7 1.8 - - - +
79B GLU* 4.4 0.2 - - - +
80B GLY* 2.9 26.0 + - - -
81B THR 3.0 22.4 + - - +
83B CYS* 3.8 9.6 - - - -
99B VAL* 3.7 32.1 - - - +
100B ARG* 1.3 76.0 - - - +
102B GLY* 1.3 60.4 + - - +
117B GLN* 3.7 28.7 - - + +
118B SER 3.6 16.8 - - - +
119B GLY* 4.1 1.1 - - - -
143B TYR* 3.9 14.6 - - + -
154B CYS* 6.0 0.9 - - - -
169B CYS* 3.8 24.0 - - - -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLU* 3.2 19.2 - - - +
100B ARG 3.7 1.6 + - - -
101B MET* 1.3 72.0 - - - +
103B ALA* 1.3 61.9 + - - -
117B GLN* 2.8 23.9 + - - -
118B SER* 2.7 22.8 + - - -
119B GLY* 4.1 0.4 - - - -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLU* 3.8 27.0 + - - +
102B GLY* 1.3 72.8 - - - -
104B ILE* 1.3 68.6 + - - +
105B ALA* 3.8 4.9 + - + +
107B MET* 4.6 2.9 - - - +
116B GLY 4.1 0.2 - - - +
117B GLN* 3.6 1.9 - - - -
118B SER* 3.4 26.5 + - - -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 3.7 30.1 - - + +
76B GLY* 4.2 3.8 - - - -
77B CYS 4.6 6.7 - - - +
102B GLY 4.0 0.2 + - - -
103B ALA* 1.3 79.2 - - - +
105B ALA* 1.3 65.9 + - - +
115B HIS* 3.8 29.4 - - + +
116B GLY 3.2 11.2 - - - +
117B GLN* 3.6 30.5 - - + +
171B VAL* 4.4 4.9 - - + -
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA* 3.8 4.4 + - + +
104B ILE* 1.3 78.6 - - - +
106B SER* 1.3 70.1 + - - +
107B MET* 3.5 17.1 - - + +
114B VAL 3.6 0.2 - - - +
115B HIS* 4.8 5.8 - - - -
116B GLY 2.8 31.3 + - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA* 1.3 77.4 - - - +
107B MET* 1.3 64.3 + - - +
113B LEU* 4.5 17.9 - - - +
114B VAL 3.4 7.1 + - - -
115B HIS* 4.5 11.2 + - - +
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Residues in contact with MET 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA 4.6 1.8 - - - +
105B ALA* 3.5 29.2 - - + +
106B SER* 1.3 79.5 - - - +
108B ARG* 1.3 60.0 + - - +
109B ILE* 3.9 18.6 - - + -
112B ARG 3.4 1.0 - - - +
113B LEU* 3.4 8.0 - - - +
114B VAL* 2.7 42.2 + - + +
116B GLY* 3.6 23.3 - - - +
117B GLN 4.0 2.5 - - - +
118B SER* 4.1 19.5 - - - +
168B VAL* 3.8 30.3 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET* 1.3 73.3 - - - +
109B ILE* 1.3 62.9 + - - +
110B GLN 4.2 0.7 + - - -
111B GLY* 3.4 34.9 + - - +
112B ARG* 3.4 4.3 - - - +
113B LEU* 3.5 41.5 - - - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET* 4.0 29.8 - - + -
108B ARG* 1.3 78.8 - - - +
110B GLN* 1.3 73.9 + - + +
112B ARG* 2.9 24.1 + - - +
114B VAL* 4.0 19.1 - - + -
159B ALA* 3.8 21.3 - - + -
168B VAL* 4.5 9.4 - - + -
203B K36 3.8 49.5 - - + +
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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