Contacts of the strand formed by residues 101 - 120 (chain B) in PDB entry 5U2H
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 SER 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B THR* 5.5 0.7 - - - -
96B PRO 4.6 0.2 - - - +
97B LEU* 3.3 8.2 - - - +
98B GLN* 2.5 46.6 + - - +
99B GLY 4.0 3.5 + - - -
100B ASN* 1.3 80.8 - - - +
102B PHE* 1.3 63.1 + - - +
316B ARG* 4.7 8.6 + - - +
317B PHE 3.1 21.8 - - - -
318B ASP* 3.6 21.2 + - - -
319B ILE 4.5 0.4 - - - +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 3.7 30.7 - - + +
65B VAL* 4.4 13.7 - - + -
94B THR* 5.2 3.4 - - - +
95B PHE 4.9 7.9 - - - +
96B PRO 5.4 1.1 - - - -
97B LEU* 4.8 4.9 - - + +
101B SER* 1.3 76.3 - - - +
103B PHE* 1.3 61.3 + - - +
104B VAL* 4.0 15.5 - - + -
190B VAL* 3.4 38.8 - - + -
192B ILE* 4.9 3.1 - - + -
254B ILE* 5.4 3.6 - - + -
316B ARG* 3.7 4.4 - - - +
317B PHE* 3.1 70.0 + + + +
319B ILE* 3.9 22.9 - - + -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR 4.8 2.7 - - - -
94B THR* 3.4 29.3 + - - -
95B PHE* 3.8 24.2 + - + +
96B PRO 5.8 0.2 + - - -
102B PHE* 1.3 73.8 - - - +
104B VAL* 1.3 69.3 + - - +
105B MET* 3.7 15.7 - - + -
291B TYR* 4.1 8.5 - + + -
293B PHE* 3.5 36.3 - + + -
312B VAL* 3.5 28.3 - - + -
314B GLY* 3.3 38.6 - - - -
315B ILE 3.8 13.0 - - - -
316B ARG* 4.1 17.0 - - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.5 16.4 - - + -
93B TYR* 3.2 20.9 - - + +
102B PHE* 4.0 13.7 - - + -
103B PHE* 1.3 84.6 - - - +
105B MET* 1.3 74.5 + - - +
106B THR* 3.6 3.6 + - + +
185B ALA* 4.6 7.6 - - + +
188B PHE* 4.4 17.0 - - + -
314B GLY* 3.3 2.1 - - - -
315B ILE* 3.1 31.0 + - + +
317B PHE* 3.6 28.0 - - + -
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 5.5 6.3 - - - -
92B ASP 4.3 16.2 - - - +
93B TYR* 2.8 32.7 + - + +
103B PHE* 3.7 15.3 - - + -
104B VAL* 1.3 81.0 - - - +
106B THR* 1.3 64.9 + - - +
107B ASN 3.9 15.5 - - - +
108B PHE* 3.7 31.4 - - + -
182B LEU* 3.6 12.2 - - + +
185B ALA* 4.5 1.6 - - - +
188B PHE* 5.3 0.5 - - - -
310B ILE* 5.2 3.6 - - + -
312B VAL* 3.7 32.3 - - + -
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Residues in contact with THR 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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104B VAL* 3.8 9.0 - - + +
105B MET* 1.3 79.9 - - - +
107B ASN* 1.3 62.2 + - - +
108B PHE* 5.6 0.7 - - - -
180B ALA* 4.1 1.4 - - - +
181B LEU 3.6 2.1 + - - -
182B LEU* 2.7 40.1 + - - +
185B ALA* 4.4 13.5 - - + -
246B ALA* 2.7 42.1 + - + -
313B PHE 3.0 11.3 + - - -
314B GLY* 3.6 4.7 - - - -
315B ILE* 3.7 34.3 - - + +
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Residues in contact with ASN 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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105B MET* 3.9 5.1 - - - +
106B THR* 1.3 74.9 + - - +
108B PHE* 1.3 76.1 + - - +
177B PRO* 3.0 53.7 + - - +
180B ALA* 3.5 17.8 - - - +
181B LEU* 3.1 21.2 - - - +
246B ALA 3.6 13.5 - - - +
247B ILE* 3.7 13.7 + - - +
313B PHE* 2.8 36.6 + - + +
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Residues in contact with PHE 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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71B VAL* 4.9 0.4 - - + -
84B VAL* 4.4 19.1 - - + -
88B PHE* 3.5 38.8 - + - -
105B MET* 3.7 26.7 - - + -
106B THR 5.6 0.7 - - - -
107B ASN* 1.3 89.2 + - - +
109B ILE* 1.3 68.8 + - - +
110B LYS* 4.3 28.3 - - + -
177B PRO* 4.5 3.6 - - - +
181B LEU* 3.6 34.2 - - + +
310B ILE* 4.3 14.6 - - + -
311B LYS 3.1 13.7 - - - +
312B VAL* 4.7 0.9 - - - -
313B PHE* 3.9 2.9 - - - -
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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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108B PHE* 1.3 80.5 - - - +
110B LYS* 1.3 68.5 - - - +
111B THR* 4.6 7.6 + - - +
171B GLU* 5.3 6.5 - - + +
172B GLU 5.3 6.7 - - - +
174B LYS* 3.1 46.2 - - + +
175B ASP 3.7 13.0 - - - +
176B ALA 4.7 0.2 - - - +
177B PRO* 4.5 9.2 - - + -
309B LEU 4.0 0.9 - - - +
310B ILE* 3.4 4.2 - - - -
311B LYS* 2.9 42.5 + - + +
313B PHE* 3.8 22.4 - - + -
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Residues in contact with LYS 110 (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 GLU* 5.8 4.0 - - - +
108B PHE* 4.2 21.1 - - + -
109B ILE* 1.3 76.4 - - - +
111B THR* 1.3 68.1 + - - +
112B GLU* 2.7 38.4 + - + +
308B THR* 4.4 5.8 - - + -
309B LEU 4.1 1.3 - - - -
310B ILE* 3.6 34.1 - - + -
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Residues in contact with THR 111 (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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109B ILE* 4.6 8.7 + - - +
110B LYS* 1.3 77.0 + - - +
112B GLU* 1.3 65.1 + - - +
114B GLN* 4.0 30.1 - - + +
169B PRO* 4.3 8.3 - - + +
170B ILE 5.0 0.9 - - - +
171B GLU* 3.8 28.6 + - - +
172B GLU 5.0 2.0 + - - +
307B ARG 4.5 0.7 - - - +
308B THR* 3.5 4.2 - - - +
309B LEU* 2.9 47.3 + - - -
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Residues in contact with GLU 112 (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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110B LYS* 2.7 42.6 + - + +
111B THR* 1.3 80.9 - - - +
113B GLY* 1.3 63.6 + - - +
114B GLN* 3.3 4.0 + - - +
169B PRO* 5.1 6.4 - - - +
299B TYR* 4.6 3.1 - - - +
308B THR* 4.0 22.0 - - + +
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Residues in contact with GLY 113 (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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112B GLU* 1.3 75.3 - - - +
114B GLN* 1.3 66.6 + - - +
115B GLN* 3.4 11.4 + - - +
168B CYS 3.7 5.4 - - - +
169B PRO* 4.6 4.2 - - - +
299B TYR* 3.4 20.6 + - - -
306B LYS* 5.1 4.0 - - - +
307B ARG 4.1 2.2 + - - -
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Residues in contact with GLN 114 (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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111B THR* 4.0 16.5 - - + +
112B GLU 3.3 1.2 + - - -
113B GLY* 1.3 78.3 - - - +
115B GLN* 1.3 57.4 + - - +
167B TRP* 3.5 35.0 - - + +
168B CYS 3.3 6.7 - - - +
169B PRO* 3.0 30.6 + - + +
170B ILE* 3.8 2.6 - - - +
171B GLU 3.4 17.8 - - - +
306B LYS* 3.4 4.0 - - - -
307B ARG* 2.9 44.0 + - + +
309B LEU* 3.1 41.2 + - - +
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Residues in contact with GLN 115 (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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113B GLY 4.1 6.8 + - - +
114B GLN* 1.3 77.5 - - - +
116B GLN* 1.3 73.9 + - - +
117B GLY* 3.2 0.7 + - - -
167B TRP* 3.7 6.7 - - - -
168B CYS* 2.9 38.1 + - + +
304B VAL* 4.7 14.4 - - - +
305B GLU 3.8 17.2 - - - +
306B LYS* 4.8 3.1 - - + -
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Residues in contact with GLN 116 (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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115B GLN* 1.3 79.4 - - - +
117B GLY* 1.3 58.4 + - - +
166B ALA 3.5 8.7 - - - +
167B TRP* 3.4 26.9 - - + -
305B GLU 4.7 3.0 + - - -
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Residues in contact with GLY 117 (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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115B GLN 3.2 2.1 + - - -
116B GLN* 1.3 75.4 - - - +
118B LEU* 1.3 60.2 + - - -
165B SER* 3.4 9.2 + - - -
166B ALA* 2.9 33.8 + - - +
168B CYS* 3.4 9.6 - - - -
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Residues in contact with LEU 118 (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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117B GLY* 1.3 73.2 - - - -
119B CYS* 1.3 64.9 + - - +
149B THR* 5.3 3.8 - - + -
163B GLU* 3.5 25.9 - - + +
164B VAL 3.3 10.5 - - - +
165B SER* 4.3 5.6 - - - +
168B CYS* 3.4 2.3 - - - +
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Residues in contact with CYS 119 (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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118B LEU* 1.3 72.0 - - - +
120B PRO* 1.3 78.0 - - + +
163B GLU* 4.2 5.9 - - - +
164B VAL* 2.9 36.9 + - - +
166B ALA 5.3 0.7 - - - -
167B TRP 3.9 6.3 - - - -
168B CYS* 2.0 54.7 - - + -
169B PRO* 4.3 7.0 - - + -
170B ILE* 4.1 15.5 - - - -
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Residues in contact with PRO 120 (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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119B CYS* 1.3 93.7 - - + +
121B ASP* 1.3 63.7 + - - +
122B PHE 3.8 0.3 + - - -
153B VAL* 3.4 36.3 - - + -
154B VAL 4.0 13.5 - - - +
155B TYR* 4.3 22.3 - - + -
161B THR* 3.9 11.2 - - - +
162B CYS 3.9 2.7 - - - +
163B GLU* 5.5 0.9 - - + -
164B VAL* 4.4 0.4 - - - -
170B ILE* 4.2 8.5 + - - +
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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
------------------------------------------------------------
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