Contacts of the strand formed by residues 900 - 908 (chain A) in PDB entry 2IVF
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 ASP 900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893A LYS* 4.4 22.9 + - + +
894A LEU 3.1 13.5 - - - +
895A PHE* 3.5 12.8 - - + +
899A ALA* 1.3 81.0 - - - +
901A CYS* 1.3 67.7 + - - +
930A LYS* 3.0 46.7 + - - -
934A ILE* 3.6 9.9 - - - +
935A LEU* 4.4 2.0 - - - -
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Residues in contact with CYS 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A LYS* 3.2 10.5 - - - +
894A LEU* 2.8 57.5 + - - -
900A ASP* 1.3 78.8 - - - +
902A GLU* 1.3 65.4 + - - +
903A ILE* 5.1 1.6 - - - -
926A TYR* 4.8 3.6 - - + -
930A LYS* 3.3 28.9 - - - +
931A PRO 3.9 6.5 - - - +
932A TYR* 3.7 25.8 - - - -
934A ILE* 4.5 0.2 - - + -
935A LEU* 4.5 4.3 - - - -
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Residues in contact with GLU 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A MET* 3.7 18.8 - - + +
892A ALA 3.2 11.0 - - - +
893A LYS* 2.6 38.6 + - + +
901A CYS* 1.3 74.7 - - - +
903A ILE* 1.3 66.5 + - - +
926A TYR* 3.8 20.6 - - - +
927A LYS* 2.9 62.4 + - + +
930A LYS 4.8 1.2 + - - -
976A ALA* 4.0 15.3 - - + +
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Residues in contact with ILE 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A PRO* 3.6 18.6 - - + -
873A VAL 3.5 24.2 - - - +
874A VAL* 3.4 29.8 - - + +
891A MET* 3.5 5.6 - - - -
892A ALA* 2.8 34.9 + - - +
894A LEU* 3.7 25.4 - - + -
901A CYS* 5.1 2.7 - - - -
902A GLU* 1.3 77.4 - - - +
904A MET* 1.3 61.6 + - - +
905A VAL 3.8 0.2 + - - -
918A VAL* 3.7 28.5 - - + -
926A TYR* 4.1 15.9 - - + -
932A TYR* 5.0 1.1 - - + -
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Residues in contact with MET 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A ARG* 3.5 42.8 - - - +
871A GLN* 3.4 39.0 - - - +
872A PRO 3.5 14.2 + - - +
873A VAL* 3.1 6.6 - - + -
874A VAL 2.7 32.1 + - - -
889A GLY 3.8 11.0 - - - +
890A ASP 3.5 9.6 - - - +
891A MET* 3.4 30.4 - - + -
903A ILE* 1.3 75.4 - - - +
905A VAL* 1.3 59.0 - - - +
124B PRO 4.7 5.4 - - - +
130B TRP* 3.8 17.0 - - + -
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Residues in contact with VAL 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A ARG* 2.9 10.2 + - - -
873A VAL* 4.4 0.2 - - - -
874A VAL* 3.5 10.8 - - + -
876A MET* 3.8 18.6 - - + -
886A ILE* 3.8 29.2 - - + -
887A LYS 4.2 4.3 - - - +
889A GLY 2.8 27.9 + - - -
890A ASP 2.7 19.1 + - - +
891A MET 4.4 0.2 - - - -
892A ALA* 3.3 33.7 - - + +
904A MET* 1.3 73.9 - - - +
906A ARG* 1.3 74.0 + - - +
907A THR* 3.8 12.3 - - + -
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Residues in contact with ARG 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A TYR* 5.9 0.4 + - - -
868A HIS* 6.2 0.8 - - - +
869A ARG* 3.4 21.9 - - - +
873A VAL* 3.4 30.7 - - + +
874A VAL 2.8 8.8 + - - +
875A HIS* 3.3 43.0 + - + +
876A MET 2.8 25.1 + - - -
888A ASP* 3.2 5.2 - - - -
905A VAL* 1.3 78.6 - - - +
907A THR* 1.3 61.8 + - - +
908A ALA* 4.8 1.8 - - + -
129B ASN 4.2 0.8 + - - -
130B TRP 2.8 26.5 + - - -
132B GLU* 2.8 47.0 + - - +
133B ASP* 4.8 1.8 - - - -
134B GLN* 3.0 24.2 + - + +
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Residues in contact with THR 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876A MET 3.3 4.3 - - - +
878A SER* 4.0 19.4 + - - +
881A ALA* 3.5 31.6 - - + -
886A ILE 4.7 0.9 - - - +
887A LYS* 4.2 1.1 - - - -
888A ASP* 3.1 41.1 + - - +
905A VAL* 3.8 8.5 - - + -
906A ARG* 1.3 73.9 - - - +
908A ALA* 1.3 63.5 + - - +
134B GLN* 3.4 21.8 + - - +
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Residues in contact with ALA 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A HIS* 5.4 1.8 - - + +
876A MET 2.9 7.1 + - - +
877A ASN* 3.3 9.7 - - - -
878A SER* 3.2 18.1 + - - -
906A ARG* 4.0 5.6 + - + +
907A THR* 1.3 76.7 - - - +
909A PRO* 1.3 73.3 - - + +
910A ASN* 3.1 27.4 + - - +
911A VAL* 3.6 9.8 + - + -
133B ASP 3.9 3.1 - - - +
134B GLN* 3.9 17.7 - - + -
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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