Contacts of the strand formed by residues 700 - 707 (chain A) in PDB entry 3LZB
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 GLY 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A SER* 3.8 0.3 - - - -
697A GLY* 3.0 29.2 + - - +
698A ALA 3.1 5.8 - - - -
699A PHE* 1.3 81.1 - - - +
701A THR* 1.3 62.9 + - - -
702A VAL* 4.4 2.4 + - - +
721A LYS* 4.9 7.9 - - - +
722A GLU 3.1 12.1 - - - -
723A LEU* 4.1 1.6 - - - -
724A ARG* 4.1 11.0 - - - -
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Residues in contact with THR 701 (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 VAL* 3.5 20.6 - - + -
695A GLY 3.2 14.1 - - - +
696A SER* 2.8 20.3 + - - +
700A GLY* 1.3 74.3 - - - -
702A VAL* 1.3 66.2 + - - +
703A TYR* 3.6 30.7 + - + +
720A ILE 3.7 0.9 - - - +
721A LYS* 3.3 3.8 - - - +
722A GLU* 2.9 35.4 + - - -
806B ASP 4.1 5.7 + - - +
808B ARG* 4.7 11.3 - - - +
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Residues in contact with VAL 702 (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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1A ITI 3.6 79.6 - - + +
693A VAL* 3.6 4.2 - - - +
694A LEU* 2.6 34.6 + - + -
695A GLY* 2.7 25.4 + - - +
696A SER* 5.9 0.2 - - - -
700A GLY 5.2 2.5 - - - +
701A THR* 1.3 76.8 - - - +
703A TYR* 1.3 64.9 + - - +
719A ALA* 5.2 0.2 - - + -
720A ILE 3.5 8.1 - - - +
721A LYS* 4.0 11.9 - - + -
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Residues in contact with TYR 703 (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 LYS* 3.3 47.4 - - + -
691A ILE 5.5 0.2 - - - -
692A LYS 3.0 24.9 - - - +
693A VAL* 3.2 26.6 - - + +
694A LEU* 3.7 7.9 - - - +
701A THR* 3.6 34.1 - - + +
702A VAL* 1.3 75.1 - - - +
704A LYS* 1.3 67.0 + - - +
719A ALA* 3.5 5.0 - - - -
720A ILE* 2.8 47.3 + - + +
722A GLU* 3.8 24.1 + - + -
806B ASP 5.1 1.6 + - - -
807B ARG* 6.0 0.2 - - - -
808B ARG* 5.7 4.2 - - - -
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Residues in contact with LYS 704 (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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691A ILE* 2.8 41.7 + - + -
692A LYS* 2.9 27.0 + - + +
694A LEU* 3.5 29.7 - - + +
703A TYR* 1.3 76.2 - - - +
705A GLY* 1.3 65.6 + - - +
706A LEU* 5.7 2.5 - - + -
717A PRO* 5.3 4.3 - - + -
718A VAL 3.7 5.8 - - - +
768A LEU* 4.1 26.0 - - + +
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Residues in contact with GLY 705 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689A LYS 3.1 13.9 - - - -
691A ILE* 4.1 2.0 - - - -
704A LYS* 1.3 78.5 - - - +
706A LEU* 1.3 72.9 + - - +
717A PRO* 3.3 2.1 - - - +
718A VAL* 2.9 30.0 + - - +
720A ILE* 3.1 18.7 - - - +
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Residues in contact with LEU 706 (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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688A PHE* 3.1 8.8 - - - -
689A LYS* 3.0 28.4 + - + +
691A ILE* 3.1 36.6 - - + -
704A LYS* 5.7 3.6 - - + -
705A GLY* 1.3 80.2 - - - +
707A TRP* 1.3 59.2 + - - +
708A ILE* 3.8 5.8 + - + +
715A LYS* 3.9 38.1 - - + +
716A ILE 3.3 3.6 - - - -
717A PRO* 3.8 24.2 - - + -
718A VAL* 3.9 3.4 - - - +
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Residues in contact with TRP 707 (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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681A ARG* 3.8 36.7 - - - +
683A LEU* 4.2 22.6 - - + +
687A GLU* 3.5 19.5 + - - +
688A PHE* 4.4 3.8 - - + +
706A LEU* 1.3 71.9 - - - +
708A ILE* 1.3 64.0 + - - +
709A PRO* 3.2 46.2 - - + +
715A LYS* 3.4 1.4 - - - -
716A ILE* 2.5 71.4 + - + +
718A VAL* 3.9 15.8 - - + +
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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