Contacts of the strand formed by residues 608 - 619 (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 TYR 608 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B ARG* 4.0 21.0 + - - +
162B VAL 3.9 5.2 - - - -
163B ILE* 3.6 27.1 - - + -
164B PRO* 3.0 43.0 - - + +
167B ARG* 3.8 36.3 - - + -
563B SER* 4.7 1.2 + - - -
604B ILE* 4.4 2.3 - - - +
606B ALA* 3.6 17.8 - - - +
607B ASP* 1.3 98.8 - - + +
609B CYS* 1.3 62.0 + - - +
610B TYR* 3.5 31.8 - + + +
632B ALA* 5.7 0.7 - - + -
633B MET 3.3 7.2 - - - +
634B PRO* 3.9 5.4 - - + -
635B THR* 3.8 4.6 - - - +
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Residues in contact with CYS 609 (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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189B VAL* 3.4 42.4 - - - -
563B SER* 3.5 15.0 - - - +
566B LEU* 3.7 15.0 - - + -
604B ILE* 4.5 7.9 - - + -
608B TYR* 1.3 74.1 - - - +
610B TYR* 1.3 69.5 + - - +
632B ALA* 3.5 0.5 - - - -
633B MET* 2.8 48.6 + - - +
635B THR* 4.2 10.5 - - + -
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Residues in contact with TYR 610 (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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167B ARG* 4.7 11.4 - - + +
241B PHE* 3.5 31.2 + + + +
254B ASN* 3.2 48.6 - - + +
255B PHE* 3.7 18.4 - - + -
563B SER* 2.7 37.8 + - - -
566B LEU* 3.4 3.5 - - - +
608B TYR* 3.5 39.6 - + + +
609B CYS* 1.3 76.4 - - - +
611B VAL* 1.3 68.4 + - - +
630B THR* 4.9 0.9 - - + -
631B LEU 3.1 7.9 - - - +
632B ALA* 3.5 29.2 - - + -
633B MET* 4.7 1.1 - - - -
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Residues in contact with VAL 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 4.0 15.0 - - + -
203B PHE* 5.6 0.2 - - + -
205B LEU* 3.3 37.9 - - + -
255B PHE* 3.9 1.6 - - - -
560B ALA* 5.2 0.7 - - + -
561B ARG 3.3 4.9 - - - +
562B GLY* 4.4 7.9 - - - -
566B LEU* 3.9 17.7 - - + -
568B MET* 5.0 9.0 - - + -
598B VAL* 5.3 3.8 - - + -
610B TYR* 1.3 80.9 - - - +
612B GLN* 1.3 68.3 + - - +
613B VAL* 4.5 3.4 - - + -
629B ILE 3.6 1.2 - - - +
630B THR* 3.4 2.1 - - - +
631B LEU* 2.8 40.8 + - + +
633B MET* 4.2 12.6 - - + -
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Residues in contact with GLN 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 3.6 7.8 + - - -
237B TYR* 2.8 56.1 + - + +
238B MET 4.2 0.2 + - - -
239B ASN* 3.8 9.5 - - - +
255B PHE* 3.3 22.5 - - + -
559B ARG 3.7 0.3 - - - +
560B ALA* 3.0 2.6 - - - -
561B ARG* 2.6 50.2 + - + +
611B VAL* 1.3 73.5 - - - +
613B VAL* 1.3 66.3 + - - +
614B ALA* 5.3 1.8 - - + +
628B ILE* 3.6 23.1 - - + +
629B ILE 3.2 2.0 - - - +
630B THR* 2.9 26.4 + - - +
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Residues in contact with VAL 613 (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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182B ILE* 4.2 20.6 - - + -
205B LEU* 5.3 0.2 - - + -
207B ILE* 3.9 29.4 - - + -
558B MET* 3.6 35.7 - - + -
559B ARG 3.2 8.3 - - - +
560B ALA* 4.2 9.6 - - + -
611B VAL* 4.5 3.4 - - + -
612B GLN* 1.3 77.9 - - - +
614B ALA* 1.3 65.1 + - - +
615B VAL* 4.5 2.7 - - + -
627B ARG 3.7 1.1 - - - +
628B ILE* 3.3 6.9 - - - +
629B ILE* 2.7 51.3 + - + +
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Residues in contact with ALA 614 (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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237B TYR* 3.7 22.0 - - + +
557B VAL 3.8 1.2 - - - +
558B MET* 3.3 1.9 - - - -
559B ARG* 2.5 48.8 + - + +
561B ARG* 4.4 12.1 - - - +
612B GLN* 5.3 1.8 - - + +
613B VAL* 1.3 75.2 - - - +
615B VAL* 1.3 62.8 + - - +
616B LEU 4.1 0.7 - - - +
626B ILE* 5.3 0.2 - - + -
627B ARG 3.6 3.8 - - - -
628B ILE* 3.7 18.4 - - + -
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Residues in contact with VAL 615 (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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209B PRO* 4.5 10.5 - - + -
210B TYR* 5.5 0.9 - - + -
556B THR* 3.2 32.3 - - + -
557B VAL 3.4 3.1 - - - +
558B MET* 3.5 35.4 - - + -
588B MET* 4.4 8.7 - - + -
613B VAL* 4.5 4.0 - - + -
614B ALA* 1.3 76.7 - - - +
616B LEU* 1.3 59.3 + - - +
617B LEU* 3.5 20.6 + - + +
626B ILE* 3.3 7.6 - - - +
627B ARG* 2.9 42.0 + - + +
629B ILE* 6.2 1.8 - - + -
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Residues in contact with LEU 616 (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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237B TYR* 5.8 3.1 - - - +
296B TYR* 4.1 24.0 - - + +
555B GLU 3.8 1.2 - - - +
556B THR* 3.1 6.2 - - - +
557B VAL* 2.9 46.4 + - + +
614B ALA 4.1 1.0 - - - -
615B VAL* 1.3 73.7 - - - +
617B LEU* 1.3 59.9 + - - +
624B ARG* 3.6 39.0 - - + +
625B ARG 3.6 13.7 - - - +
626B ILE* 3.8 19.1 - - + +
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Residues in contact with LEU 617 (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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210B TYR* 3.3 20.4 - - - +
289B GLU* 4.2 13.0 - - - +
553B CYS* 3.6 15.9 - - + -
554B MET 4.3 0.2 - - - -
555B GLU 4.5 0.2 - - - -
556B THR* 3.2 23.1 - - + +
615B VAL* 3.5 29.6 - - + +
616B LEU* 1.3 75.3 - - - +
618B SER* 1.3 56.6 + - - +
619B LEU* 3.6 26.2 - - + +
624B ARG* 3.2 14.9 + - - +
625B ARG* 2.8 59.4 + - + +
627B ARG* 4.3 5.2 - - + +
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Residues in contact with SER 618 (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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301B PRO* 3.4 15.4 - - - +
302B PRO* 3.8 19.1 - - - -
553B CYS* 3.3 0.5 - - - -
554B MET* 2.8 49.8 + - - +
555B GLU* 3.4 10.2 + - - -
617B LEU* 1.3 72.7 - - - +
619B LEU* 1.3 66.4 + - - +
623B GLN 3.2 5.2 - - - -
624B ARG* 3.1 26.2 + - - -
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Residues in contact with LEU 619 (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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210B TYR* 4.8 2.9 - - + +
215B ASP* 3.4 12.6 - - + +
301B PRO* 5.4 0.2 - - - +
339B HIS* 6.1 0.2 - - + -
553B CYS* 4.4 7.4 - - - +
554B MET* 3.7 4.9 - - - +
590B ARG* 3.4 26.2 - - - +
617B LEU* 3.6 15.6 - - + +
618B SER* 1.3 75.9 - - - +
620B ASN* 1.3 73.7 + - - +
621B ASN* 2.6 45.4 + - - +
622B SER* 3.1 12.5 + - - -
623B GLN* 2.7 16.6 + - + +
625B ARG* 3.5 38.1 - - - +
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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