Contacts of the strand formed by residues 718 - 726 (chain A) in PDB entry 5TFM
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 GLU 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716A LYS* 3.4 23.6 + - - +
717A SER* 1.3 97.3 + - - +
719A TYR* 1.3 66.9 + - - +
720A ILE* 6.3 1.1 - - + -
743A ILE 3.2 10.5 - - - +
744A THR* 3.3 27.3 + - - +
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Residues in contact with TYR 719 (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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693A SER* 3.8 24.7 - - - -
695A GLN* 2.9 32.8 + - - -
696A PHE* 3.6 28.3 - + - -
711A LEU* 4.3 5.6 - - + +
712A ASP 5.5 1.7 + - - -
716A LYS* 3.4 47.5 + - + +
718A GLU* 1.3 78.6 - - - +
720A ILE* 1.3 64.8 + - - +
721A LEU* 4.4 8.7 - - + -
741A VAL 3.6 1.3 - - - +
742A ASN* 3.4 4.3 - - - +
743A ILE* 2.9 48.3 + - + +
745A LEU* 4.1 30.4 - - + +
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Residues in contact with ILE 720 (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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692A GLY* 4.4 7.4 - - - -
718A GLU* 6.0 1.6 - - + -
719A TYR* 1.3 77.1 - - - +
721A LEU* 1.3 72.8 + - - +
722A ILE* 5.4 4.1 - - + +
740A THR* 4.5 13.0 - - + -
741A VAL 3.6 2.5 - - - -
742A ASN* 3.6 27.1 - - + +
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Residues in contact with LEU 721 (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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690A LEU* 4.2 24.0 - - + -
691A GLU 3.3 6.3 - - - +
692A GLY* 3.8 6.5 - - - -
693A SER* 3.6 35.9 - - - +
696A PHE* 4.0 21.1 - - + -
705A ILE* 5.1 3.1 - - + -
719A TYR* 4.4 8.7 - - + -
720A ILE* 1.3 78.9 - - - +
722A ILE* 1.3 64.0 + - - +
740A THR* 3.2 7.8 - - - +
741A VAL* 2.9 47.1 + - + +
743A ILE* 3.5 28.7 - - + -
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Residues in contact with ILE 722 (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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689A SER 4.5 0.2 - - - -
690A LEU* 3.4 4.5 - - - +
691A GLU* 2.8 65.4 + - + +
720A ILE* 5.4 4.7 - - + +
721A LEU* 1.3 76.8 - - - +
723A VAL* 1.3 67.9 + - - +
724A ARG* 3.9 22.7 + - - +
738A ILE* 3.9 26.7 - - + -
739A ALA 3.7 2.9 - - - +
740A THR* 5.1 10.5 - - + -
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Residues in contact with VAL 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PHE* 3.8 19.4 - - + -
670A LEU* 3.7 34.1 - - + -
688A TYR* 4.6 2.9 - - + -
689A SER 3.4 9.4 - - - +
690A LEU* 4.0 21.8 - - + -
698A ILE* 4.1 11.0 - - + -
721A LEU 5.1 0.2 - - - -
722A ILE* 1.3 78.7 - - - +
724A ARG* 1.3 65.0 + - - +
737A GLY 3.6 0.3 - - - +
738A ILE* 3.3 8.3 - - - +
739A ALA* 2.9 36.3 + - + +
741A VAL* 3.9 18.8 - - + -
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Residues in contact with ARG 724 (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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687A ILE 3.6 1.1 - - - +
688A TYR* 3.3 4.7 - - - +
689A SER* 2.8 52.9 + - - +
691A GLU* 3.2 41.5 + - - +
722A ILE* 3.9 27.1 + - + +
723A VAL* 1.3 76.4 - - - +
725A ALA* 1.3 59.7 + - - +
726A VAL* 4.8 7.4 - - + -
736A THR* 3.9 18.2 - - - +
737A GLY 3.3 2.0 - - - -
738A ILE* 4.1 23.0 - - + +
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Residues in contact with ALA 725 (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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646A PRO* 3.9 11.8 - - + +
648A PHE* 3.8 13.3 - - + -
672A ALA* 3.7 30.1 - - + -
686A ILE* 3.7 13.5 - - + -
687A ILE 3.6 5.6 - - - -
688A TYR* 4.1 3.1 - - + -
723A VAL 4.1 0.6 + - - -
724A ARG* 1.3 73.8 - - - +
726A VAL* 1.3 61.9 + - - +
736A THR* 3.2 4.9 + - - -
737A GLY 2.8 31.7 + - - +
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Residues in contact with VAL 726 (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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646A PRO* 4.1 4.3 - - - -
685A SER 3.4 2.4 - - - +
686A ILE* 3.3 4.7 - - - -
687A ILE* 2.9 55.3 + - + +
689A SER* 6.3 1.3 - - - -
724A ARG* 4.8 11.2 - - + -
725A ALA* 1.3 79.3 - - - +
727A ASP* 1.3 62.3 + - - +
734A GLN* 3.5 25.8 - - - +
735A LYS 3.4 6.3 - - - +
736A THR* 3.7 20.9 - - - +
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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