Contacts of the strand formed by residues 942 - 949 (chain B) in PDB entry 5IY8
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 LYS 942 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A ASP* 4.1 25.4 + - + +
516B GLU* 4.3 23.3 + - - -
724B TYR* 6.2 2.5 - - - -
728B MET* 3.4 31.3 - - + +
792B ASP* 3.7 17.7 - - - +
934B LYS* 3.6 33.8 - - - +
935B PHE 3.4 7.9 - - - +
936B ALA* 3.5 11.9 - - + -
940B GLY 3.7 0.6 + - - +
941B GLN* 1.3 78.3 - - - +
943B GLY* 1.3 59.4 + - - +
1051B LEU* 4.4 7.2 - - + -
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Residues in contact with GLY 943 (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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497A ASP* 4.4 7.6 - - - -
792B ASP* 3.5 15.3 - - - -
793B SER* 4.8 1.6 - - - -
794B VAL* 4.9 7.0 - - - +
934B LYS* 4.4 4.1 - - - +
935B PHE* 2.9 35.7 + - - +
941B GLN 4.0 0.2 + - - -
942B LYS* 1.3 76.5 - - - +
944B THR* 1.3 65.6 + - - -
945B CYS 3.8 0.9 + - - -
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Residues in contact with THR 944 (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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366A VAL* 4.4 6.9 - - + +
368A THR* 3.6 19.1 - - + -
496A PHE* 3.4 15.8 + - - -
497A ASP 4.2 0.3 - - - -
498A GLY* 3.7 19.1 + - - -
792B ASP 3.1 7.5 + - - -
793B SER* 2.6 31.2 - - - -
794B VAL* 3.0 8.6 + - - +
932B GLY* 3.3 37.8 + - - +
933B ASP 3.4 7.0 - - - +
934B LYS* 4.3 8.2 - - - +
943B GLY* 1.3 74.6 - - - -
945B CYS* 1.3 57.7 - - - +
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Residues in contact with CYS 945 (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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368A THR* 4.2 0.2 - - - +
794B VAL* 3.5 12.7 - - + +
796B MET* 3.9 19.7 - - - -
930B GLN* 4.1 15.9 - - - +
931B ILE* 3.2 20.2 - - - +
932B GLY 3.5 3.8 + - - -
933B ASP 3.2 15.4 + - - +
935B PHE* 3.6 24.7 - - + -
943B GLY 3.8 1.0 + - - -
944B THR* 1.3 71.4 - - - +
946B GLY* 1.3 62.7 + - - +
947B ILE 3.4 2.9 - - - -
948B GLN* 3.6 33.7 - - - -
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Residues in contact with GLY 946 (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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368A THR* 4.1 3.3 + - - -
369A PRO* 4.3 8.0 - - - +
483A ARG* 2.6 32.0 + - - -
788B TYR* 3.7 21.2 - - - -
793B SER* 3.9 11.0 - - - -
794B VAL 2.8 17.1 + - - +
931B ILE* 4.1 0.7 - - - -
944B THR 3.5 3.6 + - - -
945B CYS* 1.3 73.9 - - - +
947B ILE* 1.3 57.1 + - - +
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Residues in contact with ILE 947 (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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483A ARG* 4.7 0.9 - - - +
788B TYR* 3.4 42.2 - - + -
794B VAL 3.4 3.4 + - - +
795B ILE* 3.9 18.2 - - + -
796B MET* 3.2 20.4 + - - +
931B ILE* 3.5 18.2 - - + -
945B CYS* 3.4 1.9 - - - -
946B GLY* 1.3 76.6 + - - +
948B GLN* 1.3 82.8 + - - +
949B TYR* 3.9 20.4 - - + -
66K PRO* 3.9 28.3 - - + -
67K LEU* 5.1 9.9 - - + -
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Residues in contact with GLN 948 (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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479A TRP* 5.1 11.1 + - - -
796B MET* 2.9 17.0 - - - +
798B ARG* 4.1 36.2 + - + +
801B VAL* 3.9 22.8 - - - +
929B PRO 2.7 29.8 + - - +
930B GLN* 4.3 9.4 - - - +
931B ILE* 4.3 9.5 + - + +
945B CYS* 3.6 23.7 - - - -
947B ILE* 1.3 91.1 - - - +
949B TYR* 1.3 66.9 + - - +
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Residues in contact with TYR 949 (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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785B TYR* 3.9 22.2 - + - -
786B THR* 2.7 36.2 + - - +
788B TYR* 3.9 12.0 - - - -
795B ILE* 3.4 30.2 - - + +
796B MET 3.2 5.7 + - - -
797B ASN* 3.4 7.8 - - - +
798B ARG* 2.7 24.7 + - - -
947B ILE* 3.9 21.5 - - + +
948B GLN* 1.3 79.1 - - - +
950B ARG* 1.3 60.8 + - - +
953B ASP* 3.8 27.6 - - + -
954B MET* 3.8 15.9 - - - +
1032B PHE* 4.2 13.9 - + - -
66K PRO* 4.9 12.4 - - + +
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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