Contacts of the strand formed by residues 116 - 127 (chain B) in PDB entry 3QI5
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 GLU 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B VAL* 4.0 8.8 - - + +
109B ARG 3.3 4.5 - - - +
110B ARG* 3.8 43.0 + - + -
114B GLY 3.5 5.7 + - - +
115B THR* 1.3 76.6 - - - +
117B LEU* 1.3 65.1 + - - +
118B ARG* 2.6 39.4 + - - +
188B GLU* 4.0 27.8 - - - +
189B GLY* 4.3 1.2 - - - -
243B TRP* 4.1 11.0 - - - -
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Residues in contact with LEU 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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107B LEU 3.8 1.0 - - - +
108B VAL* 3.4 6.9 - - - +
109B ARG* 2.7 44.2 + - + +
111B LEU* 4.0 28.9 - - + -
115B THR* 3.9 10.1 - - + -
116B GLU* 1.3 72.9 - - - +
118B ARG* 1.3 61.2 + - - +
188B GLU 3.4 3.6 - - - +
189B GLY* 3.4 32.3 - - - +
192B THR* 3.8 17.5 - - + -
193B MET* 4.2 11.4 - - + -
196B LEU* 4.4 4.0 - - + -
224B ALA 3.5 24.7 - - - +
225B LEU* 3.8 19.2 - - + +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 5.7 1.0 - - - +
106B VAL* 3.6 26.0 - - + -
107B LEU 3.6 1.3 - - - -
108B VAL* 3.7 16.3 - - + +
116B GLU* 2.6 33.4 + - - +
117B LEU* 1.3 76.1 - - - +
119B GLY* 1.3 57.6 + - - +
187B LEU* 2.8 32.4 + - + -
188B GLU* 2.7 51.2 + - + +
193B MET* 3.4 11.6 - - - +
225B LEU* 5.7 0.9 - - - -
243B TRP* 4.9 0.4 - - - -
245B GLU* 2.8 43.4 + - - -
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Residues in contact with GLY 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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106B VAL* 3.5 4.2 - - - -
107B LEU* 2.8 42.1 + - - +
118B ARG* 1.3 75.5 - - - +
120B ARG* 1.3 61.5 + - - -
121B ILE 3.8 0.3 + - - -
184B LEU* 4.2 20.9 - - - +
185B GLU 3.2 12.8 - - - -
186B PRO* 4.4 1.3 - - - -
187B LEU* 4.3 0.9 - - - -
193B MET* 5.1 1.6 - - - -
225B LEU* 5.3 1.0 - - - +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLY* 3.5 31.3 + - - +
105B GLN 3.5 4.3 - - - -
106B VAL* 4.4 5.8 - - + +
119B GLY* 1.3 71.1 - - - -
121B ILE* 1.3 63.7 + - - +
122B VAL* 3.5 19.3 + - - +
184B LEU* 3.1 3.8 - - - -
185B GLU* 2.7 67.9 + - + +
187B LEU* 3.9 21.6 - - + +
248B PRO* 6.1 2.5 - - - -
249B LEU* 2.9 52.1 + - - +
251B PRO* 4.6 7.3 - - - +
279B VAL* 4.9 13.9 - - - +
282B SER* 5.7 0.2 + - - -
284B TRP* 6.0 0.2 - - - -
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Residues in contact with ILE 121 (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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102B PHE* 3.4 46.0 - - + +
103B LEU* 3.5 3.6 - - - +
104B GLY* 2.8 28.6 + - - -
105B GLN 2.9 13.4 + - - +
107B LEU* 4.5 5.8 - - + -
120B ARG* 1.3 71.7 - - - +
122B VAL* 1.3 65.8 + - - +
123B GLU 4.1 7.6 - - - +
124B THR* 3.6 30.3 - - + -
181B LEU* 3.8 20.2 - - + -
183B ALA 3.7 6.1 - - - +
184B LEU* 3.5 19.7 - - + -
244B LEU* 3.8 20.9 - - + -
279B VAL* 4.8 0.5 - - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.5 6.9 - - - +
120B ARG* 3.7 31.0 - - - +
121B ILE* 1.3 78.0 - - - +
123B GLU* 1.3 60.9 + - - +
183B ALA* 3.1 28.7 + - + +
184B LEU 4.1 2.2 - - - +
185B GLU* 4.3 9.0 - - + +
278B TYR* 3.2 5.9 - - - +
279B VAL* 3.1 39.7 + - + -
282B SER* 3.9 19.3 - - - +
284B TRP* 4.0 23.6 - - + +
285B VAL* 4.0 4.8 - - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.7 1.4 - - - +
121B ILE* 3.8 1.6 - - - +
122B VAL* 1.3 82.8 - - + +
124B THR* 1.3 69.1 + - - +
181B LEU* 4.1 0.5 - - - -
182B ARG* 2.9 55.4 + - + +
183B ALA* 3.4 19.9 + - + +
276B ARG* 2.8 31.6 + - + +
277B PHE 3.4 6.5 - - - +
278B TYR* 3.8 15.0 - - + -
285B VAL* 3.9 5.8 - - + -
286B SER* 2.6 38.5 + - - -
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Residues in contact with THR 124 (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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99B ALA* 2.6 35.7 + - - +
102B PHE* 3.8 11.2 - - + -
103B LEU* 4.2 2.9 - - + +
121B ILE* 3.6 21.8 - - + -
123B GLU* 1.3 79.1 - - - +
125B GLU* 1.3 65.3 + - - +
179B VAL* 3.9 9.6 - - + -
180B LEU 3.3 9.2 - - - +
181B LEU* 3.9 12.6 - - + -
182B ARG* 4.4 2.9 - - - +
276B ARG* 3.4 6.5 - - - +
277B PHE* 2.9 40.2 + - - +
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Residues in contact with GLU 125 (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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99B ALA* 4.3 5.2 - - - -
124B THR* 1.3 80.2 - - - +
126B ALA* 1.3 60.5 + - - +
127B TYR* 2.7 38.9 + - + -
179B VAL* 3.3 7.8 - - - +
180B LEU* 3.0 44.6 + - + +
182B ARG* 3.4 26.0 + - - +
261B ARG* 3.3 15.7 - - + -
262B VAL* 2.8 31.6 + - - +
275B LEU 3.3 4.7 - - - +
276B ARG* 3.5 15.4 - - + -
7E EDC 4.3 1.9 - - - -
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Residues in contact with ALA 126 (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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95B ALA* 3.9 32.3 - - + +
96B VAL* 4.0 9.4 - - + +
99B ALA* 4.1 7.6 - - + +
125B GLU* 1.3 72.8 - - - +
127B TYR* 1.3 61.6 + - - +
128B LEU* 4.0 11.0 - - + -
178B CYS 3.9 3.4 - - - -
179B VAL* 4.7 0.7 - - - -
261B ARG* 3.0 25.3 + - - -
275B LEU* 2.9 21.1 + - + +
277B PHE* 4.3 2.5 - - + -
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Residues in contact with TYR 127 (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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95B ALA* 4.0 1.2 - - - +
125B GLU* 2.7 44.3 + - + -
126B ALA* 1.3 74.4 - - - +
128B LEU* 1.3 61.8 + - - +
129B GLY 3.5 2.0 - - - -
132B ASP* 3.6 4.5 - - - -
134B ALA* 4.2 9.4 - - + -
135B ALA* 3.9 25.4 - - + -
149B MET* 4.8 1.3 - - + -
169B ASN* 4.4 5.6 - - - -
176B GLY 5.0 0.2 - - - -
177B ALA* 3.2 8.0 - - - +
178B CYS* 2.9 49.2 + - - +
180B LEU* 4.1 2.9 - - + -
261B ARG* 3.2 34.5 - - - +
262B VAL 4.6 1.7 + - - -
264B VAL* 6.1 1.4 - - + +
7E EDC 3.0 65.2 + + + -
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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