Contacts of the strand formed by residues 305 - 314 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D VAL* 3.4 18.1 - - + +
113D PRO* 3.7 25.6 - - + -
116D ARG* 3.8 22.9 - - + +
301D SER* 3.5 0.6 - - - -
302D VAL* 2.8 37.0 + - - +
303D GLY 3.2 2.4 + - - -
304D GLY* 1.3 77.4 - - - +
306D PRO* 1.3 68.2 - - - +
307D CYS 3.9 0.2 + - - -
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Residues in contact with PRO 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D VAL* 3.7 6.1 - - - +
116D ARG* 3.8 20.5 - - + +
127D HIS* 4.9 12.6 + - + +
128D ILE* 4.3 11.4 + - - +
300D LEU 3.5 7.2 - - - +
301D SER* 4.4 5.8 - - - +
304D GLY 3.5 8.3 - - - +
305D ALA* 1.3 86.7 - - + +
307D CYS* 1.3 64.4 + - - +
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Residues in contact with CYS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D VAL* 4.1 18.6 - - + -
127D HIS* 4.2 7.9 - - - -
128D ILE* 3.4 28.9 - - + +
130D VAL* 3.7 23.3 - - + -
299D ALA* 3.9 1.9 - - - +
300D LEU* 2.8 61.4 + - - +
302D VAL* 4.8 1.3 - - - -
306D PRO* 1.3 78.4 - - - +
308D THR* 1.3 61.7 + - - +
309D VAL* 4.6 1.3 - - - -
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Residues in contact with THR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D HIS* 2.5 32.9 + - - -
128D ILE 3.0 7.0 + - - -
129D TYR* 3.6 13.1 - - + +
130D VAL* 2.8 27.5 + - - +
297D ARG* 4.1 12.8 - - + +
298D THR 3.7 7.4 - - - +
299D ALA* 4.8 3.3 - - - +
307D CYS* 1.3 72.8 + - - +
309D VAL* 1.3 66.9 + - - +
310D LEU* 3.6 27.7 + - + +
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 4.0 24.7 - - + -
109A LEU* 4.3 6.1 - - + -
130D VAL* 3.7 20.9 - - + +
132D ASN* 4.3 5.2 - - + -
297D ARG* 3.5 4.3 - - - -
298D THR* 2.8 49.0 + - - +
300D LEU* 3.6 33.9 - - + -
308D THR* 1.3 75.6 - - - +
310D LEU* 1.3 66.4 + - - +
311D ASN* 3.6 22.2 + - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TYR* 4.5 13.9 - - + -
130D VAL 2.9 10.5 + - - +
131D LEU* 4.0 21.8 - - + -
132D ASN* 2.9 27.9 + - - +
147D VAL* 5.2 0.2 - - + -
148D GLY* 5.2 0.4 - - - -
151D GLU* 3.8 34.1 - - + -
294D VAL* 4.7 8.7 - - + -
296D SER 3.9 2.7 - - - -
297D ARG* 3.7 29.2 - - + +
308D THR* 3.6 27.4 - - + +
309D VAL* 1.3 75.0 - - - +
311D ASN* 1.3 63.7 + - - +
312D ILE* 3.4 17.6 + - + +
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Residues in contact with ASN 311 (chain D).
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* 4.3 13.7 + - - +
109A LEU* 4.1 12.3 - - - +
132D ASN* 3.1 19.4 + - - -
134D VAL* 3.6 27.2 - - + +
294D VAL* 3.5 4.9 - - - -
295D ALA* 3.0 27.0 + - + +
296D SER* 3.0 37.4 + - - +
298D THR* 5.5 0.9 - - - -
309D VAL* 3.6 14.8 - - - +
310D LEU* 1.3 70.2 - - - +
312D ILE* 1.3 59.3 + - - +
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Residues in contact with ILE 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.8 41.5 - - + -
132D ASN 2.7 13.9 + - - +
133D GLN* 3.6 3.1 - - - -
134D VAL* 2.8 31.2 + - - +
135D ASP* 3.7 3.3 + - - +
144D LEU* 4.2 11.2 - - + -
147D VAL* 3.5 34.3 - - + -
292D TYR* 4.4 3.8 - - + -
293D HIS 3.8 6.1 - - - +
294D VAL* 5.0 4.5 - - + -
310D LEU* 3.6 17.5 - - + +
311D ASN* 1.3 74.5 - - - +
313D MET* 1.3 62.5 + - - +
314D LEU* 3.8 29.6 - - + -
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Residues in contact with MET 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 3.8 19.3 - - + +
135D ASP* 3.7 31.6 - - + -
292D TYR* 3.3 3.8 - - - -
293D HIS* 2.9 69.7 + - + +
295D ALA* 4.3 9.0 - - + -
312D ILE* 1.3 72.5 - - - +
314D LEU* 1.3 63.1 + - - +
315D ASP 3.8 0.2 + - - -
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLN* 3.7 29.6 - - + +
135D ASP* 2.8 19.7 + - - +
137D PHE* 3.4 20.4 - - - -
140D ASN* 3.8 19.5 - - + -
143D ALA* 3.9 19.3 - - + -
144D LEU* 3.8 17.7 - - + -
147D VAL* 3.9 19.1 - - + -
222D TRP* 4.3 13.2 - - + -
290D VAL* 4.8 2.7 - - + -
291D LYS 3.8 4.3 - - - +
292D TYR* 4.2 4.7 - - + -
312D ILE* 3.8 20.9 - - + -
313D MET* 1.3 73.9 - - - +
315D ASP* 1.3 63.0 + - - +
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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