Contacts of the strand formed by residues 688 - 696 (chain C) 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 PHE 688 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683C LEU* 3.6 27.4 - - + -
684C LYS 3.4 19.1 - - - -
685C GLU* 2.9 26.9 - - + +
686C THR 3.5 0.9 - - - -
687C GLU* 1.3 79.5 - - + +
689C LYS* 1.3 75.5 + - - +
690C LYS* 5.0 3.6 - - + -
706C LEU 2.9 16.2 - - - +
707C TRP* 4.5 3.8 - - + -
708C ILE* 3.8 5.5 - - - +
718C VAL* 5.3 5.4 - - + -
720C ILE* 4.4 17.9 - - + -
757C CYS* 3.3 43.7 - - + -
763C GLN* 3.6 25.8 - - + -
765C ILE* 4.5 11.9 - - + -
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Residues in contact with LYS 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C GLU 5.2 0.9 - - - +
688C PHE* 1.3 87.0 - - - +
690C LYS* 1.3 83.9 + - - +
691C ILE* 2.9 18.5 - - + +
705C GLY* 3.0 1.9 - - - -
706C LEU* 2.7 38.2 + - + -
708C ILE* 4.7 6.7 - - + -
720C ILE* 4.5 2.5 - - - -
746D ASP* 5.0 9.7 + - - -
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Residues in contact with LYS 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C GLU* 5.5 2.6 + - - -
688C PHE* 5.0 4.2 - - + -
689C LYS* 1.3 92.6 + - - +
691C ILE* 1.3 66.3 + - - +
703C TYR* 3.3 54.5 - - + -
704C LYS 3.8 4.9 - - - -
705C GLY* 4.1 1.6 - - - -
720C ILE* 4.3 11.2 - - + -
722C GLU* 3.8 17.4 + - + +
763C GLN* 2.5 35.5 + - - +
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Residues in contact with ILE 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689C LYS* 2.9 40.6 - - + +
690C LYS* 1.3 79.3 - - - +
692C LYS* 1.3 103.1 + - + +
703C TYR* 5.5 0.2 - - - -
704C LYS* 2.8 26.6 + - + +
705C GLY* 4.6 0.4 - - - -
706C LEU* 3.8 32.8 - - + +
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Residues in contact with LYS 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C ILE* 1.3 109.0 + - + +
693C VAL* 1.3 66.8 + - - +
694C LEU* 4.9 4.3 - - + -
703C TYR* 3.1 13.8 - - - -
704C LYS* 2.9 47.3 + - + +
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Residues in contact with VAL 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692C LYS* 1.3 78.1 - - - +
694C LEU* 1.3 68.2 + - - +
695C GLY* 3.7 11.9 - - - +
696C SER* 4.6 3.4 - - - +
701C THR* 3.5 25.1 - - + -
702C VAL 3.6 2.7 - - - -
703C TYR* 3.2 26.2 - - + +
747D ASN* 4.5 19.1 - - - +
748D PRO* 5.7 3.6 - - + -
803D TYR* 6.3 0.4 - - + -
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Residues in contact with LEU 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ITI 3.2 73.4 - - + +
692C LYS* 4.9 4.5 - - + -
693C VAL* 1.3 80.2 - - - +
695C GLY* 1.3 55.9 + - - +
702C VAL* 2.6 20.1 + - + +
703C TYR 3.7 7.0 - - - +
704C LYS* 3.5 50.3 - - + +
768C LEU* 4.1 11.2 - - + -
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Residues in contact with GLY 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ITI 5.2 4.9 - - - -
693C VAL* 3.7 5.4 - - - +
694C LEU* 1.3 82.9 - - - +
696C SER* 1.3 61.8 + - - -
701C THR* 3.2 6.4 - - - +
702C VAL* 2.8 33.2 + - - +
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Residues in contact with SER 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693C VAL* 4.6 3.1 - - - +
695C GLY* 1.3 72.3 - - - -
697C GLY* 1.3 59.2 + - - +
700C GLY 3.6 4.3 - - - -
701C THR* 2.8 30.8 + - - +
702C VAL* 5.7 0.9 - - - -
802D ASN* 3.4 25.4 + - - -
806D ASP* 4.0 1.7 + - - -
938D ARG* 4.0 18.3 + - - +
941D ILE* 5.3 4.7 - - - +
942D ILE* 5.1 9.2 - - - +
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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