Contacts of the helix formed by residues 669 - 678 (chain A) in PDB entry 1LVK
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 669 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP* 3.3 26.9 - - - +
46A SER* 3.5 20.3 + - - -
47A TYR 4.6 1.4 + - - +
103A PHE* 3.4 35.4 - - + -
107A ARG* 4.6 9.4 + - - -
667A LEU 3.6 1.2 + - - -
668A GLU* 1.3 74.4 - - - +
670A LYS* 1.3 74.4 + - - +
672A VAL* 4.0 0.2 - - - +
673A LEU* 2.8 39.1 + - + +
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Residues in contact with LYS 670 (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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45A ASP* 3.9 21.5 - - + +
668A GLU* 3.2 1.3 - - + -
669A ASP* 1.3 85.7 + - - +
671A VAL* 1.3 66.7 + - + +
673A LEU* 4.3 0.2 - - - +
674A ASP* 3.2 27.4 + - - +
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Residues in contact with VAL 671 (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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180A GLU* 5.7 0.9 - - - +
657A ILE* 3.7 15.7 - - + +
658A PRO 4.1 1.3 - - - +
659A ASN* 3.8 18.4 - - - +
660A ASN* 3.4 26.7 - - - +
668A GLU* 3.2 34.4 + - + +
670A LYS* 1.3 78.5 - - + +
672A VAL* 1.3 63.4 + - - +
674A ASP* 3.8 5.7 + - - +
675A GLN* 2.9 41.8 + - - +
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Residues in contact with VAL 672 (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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103A PHE* 3.7 25.8 - - + -
106A LEU* 4.3 9.6 - - + -
126A VAL* 6.0 0.2 - - + -
656A ILE* 4.2 13.2 - - + -
657A ILE 3.8 12.1 - - - +
658A PRO 3.8 11.7 - - - +
667A LEU* 3.6 30.5 - - + -
668A GLU 2.9 19.4 + - - +
671A VAL* 1.3 75.2 - - - +
673A LEU* 1.3 65.6 + - - +
675A GLN* 2.9 18.6 + - - +
676A LEU* 3.0 27.2 + - + +
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Residues in contact with LEU 673 (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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45A ASP* 3.7 42.4 - - + +
47A TYR* 4.6 9.2 - - + -
99A GLU* 4.0 35.7 - - + +
103A PHE* 4.0 24.7 - - + -
669A ASP* 2.8 27.1 + - + +
672A VAL* 1.3 73.0 - - - +
674A ASP* 1.3 63.7 + - - +
676A LEU* 3.1 19.6 + - + +
677A ARG* 2.9 31.4 + - - +
682A LEU* 4.2 12.7 - - + +
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Residues in contact with ASP 674 (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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180A GLU* 4.9 8.0 - - - +
670A LYS 3.2 17.6 + - - +
671A VAL* 4.1 5.9 - - - +
672A VAL 3.1 0.6 - - - -
673A LEU* 1.3 80.2 - - - +
675A GLN* 1.3 56.0 + - - +
677A ARG* 3.3 19.7 + - - +
678A CYS* 3.0 41.8 + - - -
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Residues in contact with GLN 675 (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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180A GLU* 3.3 32.6 + - + +
655A CYS 4.3 3.6 - - - +
656A ILE* 3.4 24.1 - - + +
657A ILE* 2.7 54.6 + - - +
671A VAL* 2.9 31.2 + - - +
672A VAL 2.9 7.1 + - - +
674A ASP* 1.3 80.2 - - - +
676A LEU* 1.3 56.2 + - - +
678A CYS* 3.3 4.2 + - - +
679A ASN* 3.0 38.9 + - + +
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Residues in contact with LEU 676 (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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102A VAL* 4.9 9.2 - - + -
103A PHE* 5.1 3.6 - - + -
106A LEU* 4.1 19.1 - - + -
124A VAL* 4.9 2.2 - - + -
656A ILE* 4.1 28.7 - - + -
672A VAL* 3.0 31.2 + - + +
673A LEU* 3.1 21.7 + - + +
675A GLN* 1.3 73.8 - - - +
677A ARG* 1.3 65.2 + - - +
679A ASN* 3.3 10.3 - - - +
681A VAL* 3.4 24.7 + - + -
682A LEU* 3.0 47.5 + - + -
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Residues in contact with ARG 677 (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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44A ARG* 3.1 35.3 - - - +
45A ASP* 2.3 50.9 + - - -
99A GLU* 3.3 22.1 + - - +
573A TYR* 4.0 11.3 + - - +
574A ALA* 5.4 1.0 - - - -
673A LEU* 2.9 13.4 + - - +
674A ASP* 3.4 36.6 - - - +
676A LEU* 1.3 81.4 - - - +
678A CYS* 1.3 66.1 + - - +
679A ASN 3.4 0.5 + - - -
680A GLY* 3.7 5.5 + - - -
682A LEU* 3.8 17.7 - - + -
683A GLU 5.5 0.5 + - - -
686A ARG* 4.6 17.6 + - - +
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Residues in contact with CYS 678 (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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458A PHE* 3.6 21.4 - - + -
460A ILE* 5.3 6.7 - - - -
573A TYR* 3.5 20.2 - - - -
574A ALA* 3.9 36.1 - - + +
674A ASP* 3.0 31.4 + - - +
675A GLN* 4.0 4.7 - - - +
677A ARG* 1.3 81.1 - - - +
679A ASN* 1.3 56.7 + - + +
680A GLY 3.3 1.1 - - - -
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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