Contacts of the strand formed by residues 623 - 636 (chain B) in PDB entry 1M2V
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 GLN 623 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B MET* 3.0 33.9 - - + +
301B PRO* 4.1 3.3 - - - +
618B SER* 3.2 3.4 - - - -
619B LEU* 2.7 33.0 + - + +
621B ASN* 2.5 45.7 + - - +
622B SER* 1.3 79.4 - - - +
624B ARG* 1.3 60.3 + - - +
625B ARG* 2.5 39.0 + - + +
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Residues in contact with ARG 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B MET* 3.8 3.9 - - - +
292B ALA* 2.8 39.8 + - + +
296B TYR 2.2 36.8 + - - +
297B THR* 3.4 35.0 - - + +
298B LEU 5.2 0.8 - - - +
299B ARG 5.8 0.4 - - - -
301B PRO* 4.6 5.9 - - + +
555B GLU* 3.2 34.6 + - - +
616B LEU* 3.6 34.3 + - + +
617B LEU 3.2 11.4 + - - +
618B SER* 3.1 28.1 + - - -
622B SER 4.4 0.4 + - - -
623B GLN* 1.3 71.4 - - - +
625B ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.3 30.5 - - - +
289B GLU* 3.1 34.0 + - + -
290B TYR 3.2 13.0 - - - +
291B MET* 3.8 7.8 - - - -
292B ALA 4.1 0.4 - - - +
616B LEU* 3.6 2.8 - - - +
617B LEU* 2.8 47.3 + - + +
619B LEU* 3.5 27.3 - - - +
621B ASN* 4.1 1.8 - - - +
623B GLN* 2.5 44.2 + - + +
624B ARG* 1.3 78.8 - - - +
626B ILE* 1.3 69.3 + - - +
627B ARG* 5.5 0.4 - - - +
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Residues in contact with ILE 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE* 3.8 23.1 - - + -
237B TYR* 3.9 24.2 - - + +
289B GLU* 3.3 3.7 - - - -
290B TYR* 2.8 44.1 + - + -
292B ALA* 3.8 13.7 - - + -
296B TYR* 3.6 35.7 - - + -
614B ALA* 5.3 0.2 - - + -
615B VAL 3.3 11.9 - - - +
616B LEU* 3.8 12.3 - - + -
625B ARG* 1.3 82.7 - - - +
627B ARG* 1.3 63.3 + - - +
628B ILE* 3.9 20.2 - - + -
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Residues in contact with ARG 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B TYR* 4.2 5.9 + - - -
209B PRO* 2.8 37.7 + - - -
210B TYR* 3.4 38.4 - - - +
211B GLN 5.3 0.4 - - - +
215B ASP* 6.1 1.0 - - - -
219B PRO* 5.3 1.6 - - - +
220B PRO* 3.3 40.3 - - + +
287B VAL* 5.6 2.2 - - + -
288B MET 3.6 10.5 - - - +
289B GLU* 2.6 39.1 + - - +
613B VAL 3.7 0.9 - - - +
614B ALA* 3.6 2.6 - - - -
615B VAL* 2.9 46.6 + - + +
617B LEU* 4.3 4.0 - - + +
625B ARG* 4.2 0.8 - - - +
626B ILE* 1.3 72.5 - - - +
628B ILE* 1.3 67.5 + - - +
629B ILE* 5.0 7.7 - - + +
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Residues in contact with ILE 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TYR* 3.3 44.0 - - + -
238B MET 5.4 2.7 - - - +
286B ALA 4.1 2.2 - - - +
287B VAL* 3.4 2.9 - - - +
288B MET* 2.9 41.6 + - - +
290B TYR* 3.9 24.9 - - + -
612B GLN* 3.6 33.0 - - + +
613B VAL 3.3 1.6 - - - +
614B ALA* 3.7 16.2 - - + -
626B ILE* 3.9 8.1 - - + -
627B ARG* 1.3 76.2 - - - +
629B ILE* 1.3 73.7 + - - +
630B THR* 3.7 6.5 - - - +
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Residues in contact with ILE 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 4.1 2.0 - - + -
181B TYR* 3.9 33.4 - - + +
182B ILE* 3.8 36.5 - - + +
207B ILE* 4.9 3.8 - - + -
209B PRO* 4.5 15.9 - - + -
286B ALA 3.4 3.8 - - - -
287B VAL* 4.1 21.5 - - + -
611B VAL 3.6 1.7 - - - +
612B GLN* 3.2 2.9 - - - -
613B VAL* 2.7 58.2 + - + +
615B VAL* 6.2 1.3 - - + -
627B ARG* 5.0 8.7 - - + -
628B ILE* 1.3 81.0 - - - +
630B THR* 1.3 61.0 + - - +
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Residues in contact with THR 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASN* 3.8 1.6 - - - +
177B ALA* 3.3 9.1 + - - +
239B ASN* 3.6 34.6 - - + +
240B PRO* 5.1 0.2 - - - +
241B PHE* 4.1 14.4 - - + -
254B ASN* 4.7 1.1 - - - +
255B PHE* 3.9 21.3 - - + -
286B ALA* 2.8 40.4 + - - +
610B TYR* 4.9 0.4 - - + -
611B VAL 3.4 2.5 - - - +
612B GLN* 2.9 24.5 + - - +
628B ILE* 3.7 5.4 - - - +
629B ILE* 1.3 73.0 - - - +
631B LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 3.5 33.4 - - + -
176B ASN* 3.7 5.2 - - - +
177B ALA* 3.9 20.2 - - + +
182B ILE* 4.1 33.7 - - + +
184B SER* 4.1 16.6 - - - +
205B LEU* 4.7 2.9 - - + -
610B TYR* 3.1 8.5 - - - +
611B VAL* 2.8 40.9 + - + +
630B THR* 1.3 76.7 - - - +
632B ALA* 1.3 63.0 + - - +
633B MET* 3.8 32.4 + - + +
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Residues in contact with ALA 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 3.9 7.1 - - - +
163B ILE* 3.8 15.4 - - + +
176B ASN* 3.0 24.9 + - - +
241B PHE* 3.5 34.0 - - + -
608B TYR* 5.6 1.3 - - + -
609B CYS 3.5 4.3 - - - -
610B TYR* 3.5 23.1 - - + -
631B LEU* 1.3 72.9 - - - +
633B MET* 1.3 64.9 + - - +
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Residues in contact with MET 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.0 11.0 - - + -
163B ILE* 4.2 3.1 - - - -
184B SER* 3.5 32.3 - - - -
186B LEU 3.8 2.5 - - - +
187B ASN 4.3 4.0 - - - +
189B VAL* 3.6 24.5 - - + -
203B PHE* 4.3 6.1 - - + -
205B LEU* 5.1 0.7 - - + -
566B LEU* 4.1 15.3 - - + -
608B TYR* 3.3 3.4 - - - +
609B CYS* 2.8 57.7 + - - +
611B VAL* 4.2 17.5 - - + -
631B LEU* 3.8 20.2 - - + +
632B ALA* 1.3 79.8 - - - +
634B PRO* 1.3 68.9 - - + +
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Residues in contact with PRO 634 (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 ARG* 4.0 9.6 - - - +
135B MET* 3.6 23.8 - - + -
161B LEU* 4.7 1.8 - - + -
162B VAL* 2.8 44.9 - - + +
163B ILE* 3.5 7.9 - - + -
187B ASN 3.1 22.4 - - - +
188B ALA* 3.2 5.7 - - - -
189B VAL* 2.8 24.2 + - - -
607B ASP 3.5 6.3 - - - +
608B TYR* 3.9 5.2 - - + -
632B ALA 4.5 0.7 - - - +
633B MET* 1.3 83.7 - - - +
635B THR* 1.3 60.0 + - - +
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Residues in contact with THR 635 (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 ARG* 2.4 35.5 + - - -
189B VAL 3.2 10.1 - - - +
191B LYS* 3.6 17.6 + - - +
604B ILE* 3.9 19.5 - - + -
606B ALA 2.8 29.5 + - - +
607B ASP* 2.7 27.6 + - - -
608B TYR 3.7 15.0 - - - +
609B CYS* 4.0 10.1 - - + +
634B PRO* 1.3 73.4 - - - +
636B THR* 1.3 62.2 + - - +
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Residues in contact with THR 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 4.4 2.0 - - - +
188B ALA* 3.9 21.3 - - + -
189B VAL 3.0 11.7 + - - +
190B PRO* 3.5 0.2 - - - +
191B LYS* 2.8 24.3 + - - +
195B LEU* 3.3 6.1 - - - +
635B THR* 1.3 81.7 + - - +
637B GLU* 1.3 61.8 + - - +
638B SER* 2.9 17.9 + - - -
641B GLU* 2.9 34.9 + - + +
642B VAL* 4.0 19.5 - - + -
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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