Contacts of the strand formed by residues 148 - 154 (chain B) in PDB entry 3QI6
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 THR 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B HIS* 2.6 35.3 + - - +
105B VAL* 3.8 14.4 - - + +
144B ILE* 3.5 11.9 - - + +
145B ARG 2.7 33.4 + - - +
147B THR* 1.3 76.6 + - - +
149B ARG* 1.3 79.1 + - - +
150B LEU 3.3 28.9 - - - +
151B ILE* 4.7 0.7 - - + -
176B SER 4.4 1.7 - - - +
178B ALA* 3.7 15.5 - - + +
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.9 20.5 - - - +
98B LEU* 4.0 7.6 - - + -
102B ASP* 3.6 30.8 + - - +
103B HIS 3.2 3.8 + - - -
145B ARG 5.5 0.2 + - - -
146B PRO 2.9 26.9 + - - -
147B THR* 3.1 11.3 + - - +
148B THR* 1.3 94.8 + - - +
150B LEU* 1.3 60.0 - - - +
176B SER 3.7 8.9 + - - -
177B SER* 2.9 27.3 + - - +
178B ALA* 3.6 7.4 - - - +
179B LYS* 3.0 26.7 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.8 31.2 - - + -
97B MET* 3.8 39.7 - - + -
98B LEU* 4.0 22.2 - - + -
103B HIS 3.7 2.8 + - - -
104B VAL* 3.2 11.3 - - + -
105B VAL 3.0 22.7 + - - -
148B THR* 3.3 6.9 - - - +
149B ARG* 1.3 79.8 - - - +
151B ILE* 1.3 74.2 + - - +
152B TRP* 3.8 15.5 - - + -
178B ALA* 4.8 0.2 - - - -
179B LYS* 3.5 20.4 - - + +
181B LEU* 4.2 11.4 - - + -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.5 30.3 - - + +
134B LEU* 4.8 3.8 - - + -
140B VAL* 4.5 7.2 - - + -
144B ILE* 3.9 28.0 - - + -
148B THR* 4.7 0.4 - - + -
150B LEU* 1.3 79.2 - - - +
152B TRP* 1.3 62.2 + - - +
153B VAL* 3.9 8.9 + - + -
169B ILE* 3.4 32.5 - - + +
172B LEU 4.6 0.4 - - - -
173B GLY* 4.0 26.2 - - - +
178B ALA* 4.3 10.3 - - + -
179B LYS 3.1 8.3 + - - +
180B VAL* 3.6 7.3 - - + +
181B LEU 3.1 26.7 + - - +
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Residues in contact with TRP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.6 37.9 - - + -
93B ALA* 4.2 4.5 - - + -
94B LEU* 3.7 28.9 - - + -
104B VAL* 4.0 10.0 - - + +
105B VAL 2.8 15.9 + - - +
106B ILE* 3.8 9.8 - - + -
107B PRO* 3.2 37.1 - - + +
114B THR* 3.5 35.3 + - + +
118B ILE* 4.8 2.2 - - + -
134B LEU* 4.2 4.3 - - - +
150B LEU* 3.8 20.2 - - + -
151B ILE* 1.3 70.3 - - - +
153B VAL* 1.3 65.7 + - - +
154B GLU* 4.7 5.3 - - + +
181B LEU* 3.8 42.8 - - + +
183B ASP* 4.5 14.1 - - + +
203B LEU* 4.4 6.3 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.6 16.6 - - + -
151B ILE* 3.9 8.3 - - + +
152B TRP* 1.3 77.4 - - - +
154B GLU* 1.3 62.3 + - - +
155B THR* 4.1 15.0 - - + -
164B ALA* 3.9 17.3 - - + -
166B ILE* 4.6 6.3 - - + -
169B ILE* 3.8 37.7 - - + -
180B VAL* 4.1 9.9 - - + -
181B LEU 3.0 15.6 + - - +
182B VAL* 3.3 14.5 - - + +
183B ASP* 2.9 26.9 + - - +
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Residues in contact with GLU 154 (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 PRO* 4.1 10.3 - - + +
110B ALA* 3.6 10.3 - - - +
111B TYR* 2.6 45.2 + - - +
114B THR* 4.3 4.5 + - - -
134B LEU* 4.0 12.4 - - - +
152B TRP* 4.7 5.8 + - - +
153B VAL* 1.3 73.5 - - - +
155B THR* 1.3 65.8 + - - +
156B PRO 4.1 5.0 - - - +
157B THR* 3.5 23.4 - - + +
158B ASN 3.4 23.9 + - - -
162B SER 4.7 0.3 - - - +
164B ALA* 4.3 1.4 - - - +
183B ASP* 3.8 27.6 - - + +
208B LLP 3.9 13.9 - - + +
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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
------------------------------------------------------------
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