Contacts of the strand formed by residues 305 - 314 (chain A) in PDB entry 4IRQ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.5 21.6 - - + +
113A PRO* 3.6 19.3 - - + -
116A ARG* 3.5 25.7 - - + +
300A LEU 4.0 0.2 - - - +
301A SER* 3.4 0.6 - - - -
302A VAL 2.6 39.8 + - - +
303A GLY 3.2 2.4 + - - -
304A GLY* 1.3 74.2 - - - +
306A PRO* 1.3 66.5 - - + +
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLU* 5.3 2.0 - - + +
112A VAL* 3.9 6.1 - - - +
116A ARG* 3.6 26.2 - - + +
127A HIS* 5.5 8.4 - - + -
128A ILE* 4.6 9.0 + - - +
300A LEU 3.4 7.4 - - - +
301A SER* 4.1 7.6 - - - +
304A GLY 3.4 8.7 - - - +
305A ALA* 1.3 88.5 - - + +
307A CYS* 1.3 65.8 + - - +
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Residues in contact with CYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 4.1 19.1 - - + -
127A HIS* 4.1 8.0 - - - -
128A ILE* 3.4 28.3 - - + +
130A VAL* 3.8 23.1 - - + -
299A ALA* 3.8 3.6 - - - +
300A LEU* 2.8 58.4 + - - -
302A VAL* 4.8 1.8 - - - -
306A PRO* 1.3 78.4 - - - +
308A THR* 1.3 64.5 + - - +
309A VAL* 4.5 1.3 - - - -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 4.5 4.4 - - + -
127A HIS* 2.8 28.1 + - - -
128A ILE 3.0 7.9 + - - -
129A TYR* 3.4 19.8 - - + +
130A VAL* 2.8 25.9 + - - +
297A ARG* 4.1 15.7 - - + -
298A THR 3.8 7.9 - - - +
299A ALA* 5.2 3.2 - - - +
307A CYS* 1.3 75.7 + - - +
309A VAL* 1.3 63.1 + - - +
310A LEU* 3.6 24.4 + - + -
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 3.5 21.1 - - + +
132A ASN* 3.9 15.5 - - + -
297A ARG* 3.4 4.3 - - - -
298A THR* 2.9 46.7 + - + +
300A LEU* 3.8 35.4 - - + -
307A CYS* 4.1 0.4 - - - -
308A THR* 1.3 72.4 - - - +
310A LEU* 1.3 63.6 + - - +
311A ASN* 3.6 21.7 + - - +
105D PHE* 4.0 13.0 - - + -
109D LEU* 3.8 13.9 - - + -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 4.3 16.2 - - + -
130A VAL 2.8 15.2 + - - +
131A LEU* 3.7 20.6 - - + -
132A ASN* 2.8 30.0 + - - +
148A GLY* 4.8 1.1 - - - -
151A GLU* 3.6 31.4 - - + +
294A VAL* 4.5 5.8 - - + -
296A SER 3.8 1.6 - - - -
297A ARG* 3.5 45.5 - - + +
308A THR* 3.9 14.8 - - + +
309A VAL* 1.3 71.0 - - - +
311A ASN* 1.3 63.7 + - - +
312A ILE* 3.4 17.8 + - + +
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Residues in contact with ASN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASN* 2.9 26.9 + - - -
134A VAL* 3.8 17.0 - - + +
294A VAL* 3.3 4.2 - - - -
295A ALA* 2.7 38.8 + - + +
296A SER* 2.8 42.3 + - - +
298A THR* 5.7 0.4 - - - -
309A VAL* 3.6 13.7 - - - +
310A LEU* 1.3 68.4 - - - +
312A ILE* 1.3 58.0 + - - +
106D GLU* 4.2 16.2 + - - +
109D LEU* 3.8 12.7 - - - +
110D VAL* 6.3 0.6 - - - +
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.7 40.8 - - + -
132A ASN 2.8 12.9 + - - +
133A GLN* 3.7 3.6 - - - +
134A VAL* 3.0 26.9 + - - +
135A ASP* 3.7 3.3 - - - +
144A LEU* 3.9 13.2 - - + -
147A VAL* 3.6 35.2 - - + -
292A TYR* 4.4 4.5 - - + -
293A HIS 3.9 3.6 - - - +
294A VAL* 4.8 5.6 - - + -
310A LEU* 3.7 19.5 - - + +
311A ASN* 1.3 76.5 - - - +
313A MET* 1.3 62.2 + - - +
314A LEU* 3.6 28.5 - - + -
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 3.7 34.1 - - + +
135A ASP* 3.7 17.9 - - + -
292A TYR* 3.1 4.3 - - - -
293A HIS* 2.9 68.2 + - + +
295A ALA* 4.2 9.9 - - + -
312A ILE* 1.3 71.9 - - - +
314A LEU* 1.3 63.4 + - - +
315A ASP 3.7 0.2 + - - -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.7 26.7 - - + +
135A ASP* 2.5 18.7 + - - +
137A PHE* 3.2 25.5 - - - -
140A ASN* 3.8 22.2 - - + -
143A ALA* 3.9 21.1 - - + +
144A LEU* 3.9 11.4 - - + -
147A VAL* 3.9 18.4 - - + -
222A TRP* 4.2 12.8 - - + -
290A VAL* 4.8 2.5 - - + -
291A LYS 3.8 4.5 - - - +
292A TYR* 3.9 5.8 - - + -
312A ILE* 3.6 24.9 - - + -
313A MET* 1.3 71.7 - - - +
315A ASP* 1.3 59.5 + - - +
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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
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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