Contacts of the strand formed by residues 140 - 148 (chain B) in PDB entry 1I3R
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 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PRO* 3.5 7.4 - - - +
130B THR* 3.4 37.3 + - - +
131B LYS* 5.4 11.4 - - + +
139B ASN* 1.3 88.9 + - + +
141B LEU* 1.3 60.6 + - - +
142B VAL* 4.0 0.9 - - + -
169B VAL* 5.7 3.4 - - + -
186B MET* 3.5 40.8 - - + -
187B LEU 3.4 10.1 - - - +
188B GLU* 3.6 33.9 - - + +
191B PRO* 5.0 2.5 - - - +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.3 2.5 - - + -
128B TYR 3.9 4.0 - - - -
129B PRO* 4.0 20.0 - - + -
140B LEU* 1.3 75.2 - - - +
142B VAL* 1.3 58.7 + - - +
157B TRP* 3.0 40.7 - - + -
186B MET* 3.4 1.4 - - - -
187B LEU* 3.0 31.2 + - + +
189B THR* 4.8 4.7 - - - +
191B PRO* 5.3 4.0 - - + -
197B TYR* 3.2 50.5 - - + -
214B TRP* 3.7 37.2 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR 3.7 0.2 - - - +
127B VAL* 3.4 4.3 - - - -
128B TYR* 2.7 63.1 + - + +
130B THR* 3.4 38.6 - - + +
141B LEU* 1.3 69.7 - - - +
143B CYS* 1.3 64.9 + - - +
144B SER 3.6 1.1 + - - +
157B TRP* 4.1 1.8 - - - -
184B LEU* 4.1 24.7 - - + -
186B MET* 3.9 32.3 - - + -
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Residues in contact with CYS 143 (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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125B VAL* 4.0 17.7 - - - -
126B THR 3.6 4.0 - - - -
127B VAL* 4.5 1.6 - - - -
141B LEU 3.5 1.2 + - - -
142B VAL* 1.3 73.9 - - - +
144B SER* 1.3 58.2 + - - +
145B VAL* 3.9 8.6 + - - +
155B VAL* 4.2 5.4 - - - -
157B TRP* 3.3 14.6 - - + +
183B THR 4.0 0.3 - - - +
184B LEU* 3.5 2.4 - - - -
185B VAL* 2.7 50.9 + - + +
199B CYS* 2.0 49.4 - - + -
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Residues in contact with SER 144 (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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96A PRO* 3.3 27.6 - - - +
124B THR 3.5 2.1 + - - +
125B VAL* 3.3 6.1 - - - +
126B THR* 2.8 43.8 + - - -
128B TYR* 4.2 19.7 - - - -
142B VAL* 3.6 1.4 + - - -
143B CYS* 1.3 72.9 - - - +
145B VAL* 1.3 65.5 + - - +
146B SER* 4.1 1.6 + - - -
183B THR 3.9 3.8 - - - -
184B LEU* 3.7 20.1 - - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 3.6 20.9 - - + -
124B THR 3.8 2.5 - - - -
125B VAL* 4.3 4.5 - - + +
143B CYS* 4.2 11.9 - - - +
144B SER* 1.3 79.4 + - - +
146B SER* 1.3 60.9 - - - +
148B PHE* 3.6 3.4 - - + -
153B ILE* 3.2 31.0 - - + -
155B VAL* 4.0 16.4 - - + -
182B GLN* 3.3 1.9 - - - -
183B THR* 2.8 47.6 + - + +
185B VAL* 5.6 0.2 - - + -
201B VAL* 3.8 27.4 - - + -
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Residues in contact with SER 146 (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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94A ARG 4.8 0.2 - - - -
95A SER* 4.3 7.9 - - - -
96A PRO* 3.1 36.9 - - - +
123B PRO* 3.3 2.9 - - - +
124B THR* 3.0 39.9 + - - +
144B SER* 4.5 1.1 + - - -
145B VAL* 1.3 76.7 - - - +
147B ASP* 1.3 73.5 + - - +
148B PHE* 3.5 3.8 - - - -
181B PHE 3.6 4.5 - - - -
182B GLN* 3.9 13.9 - - - +
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Residues in contact with ASP 147 (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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94A ARG* 2.9 43.6 + - - +
95A SER* 5.6 6.2 - - - -
121B VAL* 3.6 16.6 - - - +
122B GLU 3.1 16.6 - - - +
124B THR* 4.7 8.7 - - - +
146B SER* 1.3 81.3 - - - +
148B PHE* 1.3 56.3 + - - +
176B ASN* 5.2 1.7 - - - +
180B THR* 3.8 15.7 + - - +
181B PHE 2.9 13.5 + - - -
182B GLN* 4.5 0.6 - - - +
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Residues in contact with PHE 148 (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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121B VAL* 3.2 15.7 - - - +
123B PRO* 3.6 18.2 - - + -
145B VAL* 3.6 34.8 - - + -
146B SER 3.9 5.8 - - - -
147B ASP* 1.3 75.1 - - - +
149B TYR* 1.3 62.5 - - - +
150B PRO 3.3 18.8 - - - -
151B GLY 4.0 1.1 - - - -
153B ILE* 3.7 35.9 - - + -
173B LEU* 3.7 18.6 - - + -
180B THR* 3.6 2.5 - - - -
181B PHE* 2.9 58.6 + - + +
182B GLN* 3.8 4.9 - - - -
183B THR* 4.3 4.3 - - + -
203B HIS* 3.5 10.1 - + - +
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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