Contacts of the strand formed by residues 305 - 314 (chain B) in PDB entry 4IRP
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 ALA 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B TRP* 3.5 17.2 - - + -
112B VAL* 3.3 11.7 - - + +
113B PRO* 3.6 25.1 - - + -
116B ARG* 3.8 12.8 - - + -
300B LEU 3.9 0.2 - - - +
301B SER* 3.4 1.4 - - - -
302B VAL 2.9 37.3 + - - +
303B GLY 3.2 2.4 + - - -
304B GLY* 1.4 75.2 - - - +
306B PRO* 1.4 66.8 - - - +
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Residues in contact with PRO 306 (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 ILE* 6.2 0.7 - - + -
84B TRP* 4.7 4.3 - - + -
112B VAL* 3.7 5.7 - - - +
116B ARG* 3.7 39.5 + - - +
127B HIS* 6.5 1.3 - - + -
128B ILE* 4.4 5.7 + - - +
300B LEU 3.5 8.3 - - - +
301B SER* 4.0 9.4 - - - +
304B GLY 3.6 8.3 - - - +
305B ALA* 1.4 85.5 - - - +
307B CYS* 1.3 66.0 + - - +
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Residues in contact with CYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 5.2 0.2 - - - -
112B VAL* 4.0 19.1 - - + -
127B HIS* 4.6 4.0 - - - -
128B ILE* 3.4 32.8 - - + +
130B VAL* 3.8 20.6 - - + -
299B ALA* 3.9 2.6 - - - +
300B LEU* 2.9 62.1 + - - +
302B VAL* 5.0 0.9 - - - -
306B PRO* 1.3 79.3 - - - +
308B THR* 1.3 61.5 + - - +
309B VAL* 4.5 1.1 - - - -
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Residues in contact with THR 308 (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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127B HIS* 2.6 34.1 + - - -
128B ILE 3.0 5.1 + - - -
129B TYR* 3.5 15.6 - - + +
130B VAL* 2.8 26.4 + - - +
297B ARG* 4.7 9.2 - - + -
298B THR 3.5 9.6 - - - +
299B ALA* 4.8 2.2 - - - +
307B CYS* 1.3 73.9 + - - +
309B VAL* 1.3 64.9 + - - +
310B LEU* 3.7 24.1 + - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.9 15.5 - - + -
109A LEU* 3.9 15.3 - - + -
130B VAL* 3.5 14.8 - - + +
132B ASN* 3.9 14.6 - - + -
296B SER 3.7 0.5 - - - +
297B ARG* 3.2 6.8 - - - -
298B THR* 2.8 49.6 + - - +
300B LEU* 3.7 33.0 - - + -
307B CYS* 4.5 0.2 - - - -
308B THR* 1.3 73.5 - - - +
310B LEU* 1.3 62.5 + - - +
311B ASN* 3.7 21.6 + - - +
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Residues in contact with LEU 310 (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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129B TYR* 4.2 17.9 - - + -
130B VAL 2.8 13.8 + - - +
131B LEU* 3.8 21.3 - - + -
132B ASN* 2.7 34.9 + - - +
147B VAL 5.3 0.2 - - - +
148B GLY* 4.9 2.2 - - - -
151B GLU* 3.7 30.5 - - + +
294B VAL* 4.5 7.0 - - + -
296B SER 3.7 2.5 - - - -
297B ARG* 3.5 38.6 - - + +
308B THR* 3.9 19.7 - - + +
309B VAL* 1.3 72.8 - - - +
311B ASN* 1.3 59.8 + - - +
312B ILE* 3.4 18.0 + - + +
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Residues in contact with ASN 311 (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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106A GLU* 4.1 17.6 + - - +
109A LEU* 4.0 12.7 - - - +
132B ASN* 2.5 38.5 + - - +
134B VAL* 3.5 19.6 - - + +
294B VAL* 3.6 2.8 - - - -
295B ALA* 2.7 37.0 + - + +
296B SER* 2.9 37.9 + - - +
298B THR* 5.5 1.1 - - - -
309B VAL* 3.7 10.0 + - - +
310B LEU* 1.3 67.7 - - - +
312B ILE* 1.3 57.7 + - - +
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Residues in contact with ILE 312 (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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131B LEU* 4.1 28.7 - - + -
132B ASN 2.9 12.7 + - - +
133B GLN* 3.7 1.0 - - - -
134B VAL* 3.0 26.8 + - - +
135B ASP* 3.6 5.7 + - - +
144B LEU* 4.0 20.2 - - + -
147B VAL* 3.6 35.7 - - + -
292B TYR* 4.4 2.7 - - + -
293B HIS 3.8 7.2 - - - +
294B VAL* 4.7 3.8 - - + +
310B LEU* 3.7 20.6 - - + +
311B ASN* 1.3 73.4 - - - +
313B MET* 1.3 62.2 + - - +
314B LEU* 3.6 32.8 - - + +
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Residues in contact with MET 313 (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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134B VAL* 3.6 30.5 - - + +
135B ASP* 3.8 19.1 - - + -
136B HIS* 6.2 2.7 - - + -
292B TYR* 3.3 1.6 - - - -
293B HIS* 2.9 68.0 + - + +
295B ALA* 4.0 16.8 - - + -
312B ILE* 1.3 71.0 - - - +
314B LEU* 1.3 64.9 + - - +
315B ASP* 3.7 2.9 + - - +
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Residues in contact with LEU 314 (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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133B GLN* 3.7 28.9 - - - +
135B ASP* 3.0 19.1 + - - +
137B PHE* 3.1 23.6 - - - -
140B ASN* 3.8 20.4 - - + -
143B ALA* 3.8 20.0 - - + -
144B LEU* 4.0 9.6 - - + -
147B VAL* 3.7 19.7 - - + -
222B TRP* 4.2 13.5 - - + -
290B VAL* 4.5 2.5 - - + -
291B LYS 3.9 5.4 - - - +
292B TYR* 4.0 6.1 - - + -
312B ILE* 3.6 24.0 - - + -
313B MET* 1.3 75.5 - - - +
315B ASP* 1.3 61.2 + - - +
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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