Contacts of the strand formed by residues 752 - 759 (chain B) in PDB entry 2IVS
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 752 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723B ASN 4.7 3.6 - - - -
725B VAL* 4.9 12.4 - - + +
742B THR* 3.9 31.2 - - + -
743B ALA 3.4 3.4 - - - -
744B PHE* 3.4 46.9 - + + +
749B ARG* 4.8 2.3 + - - -
750B ALA 3.6 3.8 + - - +
751B GLY* 1.3 75.0 - - - -
753B THR* 1.3 61.5 + - - +
754B THR* 4.2 1.0 + - - -
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Residues in contact with THR 753 (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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742B THR* 3.4 3.4 - - - -
743B ALA* 2.9 34.5 + - - +
746B LEU* 3.8 29.8 + - + +
749B ARG* 2.8 51.0 + - - +
750B ALA 4.7 0.9 + - - -
751B GLY 4.9 0.5 + - - -
752B TYR* 1.3 74.0 - - - +
754B THR* 1.3 74.8 + - - +
755B VAL* 3.5 2.3 + - + +
791B TYR* 4.6 9.4 - - - +
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Residues in contact with THR 754 (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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740B LYS* 3.7 24.7 - - + -
741B ALA 3.4 12.3 + - - +
742B THR* 4.5 10.2 - - + +
752B TYR 4.1 1.7 + - - -
753B THR* 1.3 80.7 - - - +
755B VAL* 1.3 62.4 + - - +
791B TYR* 4.9 2.3 + - - -
806B TYR* 3.7 40.3 + - + +
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Residues in contact with VAL 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B LEU* 4.1 8.7 - - + -
740B LYS* 3.7 4.2 - - - +
741B ALA* 2.8 51.4 + - + +
743B ALA* 4.1 4.9 - - + -
746B LEU* 3.6 31.2 - - + -
753B THR* 3.8 7.0 - - + +
754B THR* 1.3 79.1 - - - +
756B ALA* 1.3 59.7 + - - +
757B VAL* 4.0 6.5 - - + -
791B TYR* 3.6 14.1 - - + -
803B ILE* 3.7 20.2 - - + -
804B VAL 3.4 9.0 - - - +
806B TYR* 3.8 14.2 - - - +
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Residues in contact with ALA 756 (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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730B LEU* 4.4 3.1 - - + -
738B VAL* 4.1 13.0 - - + -
739B VAL 3.4 5.8 - - - +
740B LYS* 4.7 0.4 - - - +
755B VAL* 1.3 75.7 - - - +
757B VAL* 1.3 62.9 + - - +
803B ILE* 3.7 2.8 - - - -
804B VAL* 2.8 40.4 + - + +
805B GLU 4.2 0.9 - - - +
806B TYR* 4.1 1.9 - - + +
3016B ACK 3.5 43.5 - - + +
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Residues in contact with VAL 757 (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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724B LEU* 4.2 10.5 - - + -
726B LEU* 3.8 10.3 - - + -
737B LYS 3.7 1.4 - - - +
738B VAL* 3.3 5.5 - - - -
739B VAL* 2.8 43.0 + - + +
741B ALA* 3.6 27.4 - - + -
755B VAL* 4.0 8.3 - - + -
756B ALA* 1.3 80.2 - - - +
758B LYS* 1.3 64.2 + - - +
759B MET* 3.5 20.7 - - + +
801B LEU* 3.8 26.7 - - + -
802B LEU 3.2 10.5 - - - +
803B ILE* 4.5 3.8 - - + -
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Residues in contact with LYS 758 (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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735B PHE* 4.1 16.7 - - + -
737B LYS 3.5 3.4 - - - +
738B VAL* 3.7 22.7 - - + -
757B VAL* 1.3 75.7 - - - +
759B MET* 1.3 62.6 + - - +
772B LEU* 4.5 2.9 - - - +
775B GLU* 2.9 36.9 + - - +
800B LEU 4.0 0.2 - - - +
801B LEU* 3.4 6.1 - - - -
802B LEU* 2.9 50.4 + - + +
804B VAL* 4.5 22.4 - - + -
891B SER* 5.2 3.6 - - - -
892B ASP* 4.8 10.1 + - - +
3015B FMT 2.7 25.7 + - - +
3016B ACK 4.1 21.1 - - - -
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Residues in contact with MET 759 (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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726B LEU* 4.1 13.5 - - + -
735B PHE* 4.7 1.7 - - - -
736B GLY* 3.3 4.9 - - - -
737B LYS* 2.8 46.4 + - + +
739B VAL* 3.6 36.1 - - + -
757B VAL* 3.5 32.8 - - + +
758B LYS* 1.3 76.6 - - - +
760B LEU* 1.3 66.0 + - - +
772B LEU* 4.3 8.3 - - - -
799B PRO* 5.5 5.6 - - + -
800B LEU 3.9 7.4 - - - +
801B LEU* 3.7 21.5 - - + -
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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