Contacts of the helix formed by residues 704 - 712 (chain I) in PDB entry 4LLG
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 MET 704 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL* 3.6 30.5 - - + -
27I LEU* 5.0 0.7 - - + -
577I VAL* 4.3 7.9 - - + -
658I GLN* 3.5 28.7 - - - +
663I VAL* 3.8 23.3 - - + -
666I SER* 3.5 37.5 - - - +
667I LEU* 3.7 13.2 - - + -
702I THR* 2.9 10.5 + - - +
703I GLY* 1.3 79.1 - - - +
705I GLU* 1.3 57.6 + - - +
706I ARG 3.4 1.3 - - - -
707I ALA* 3.1 17.6 + - + +
708I VAL* 2.9 32.6 + - + +
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Residues in contact with GLU 705 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ARG* 4.3 18.3 - - - +
667I LEU* 3.7 13.6 - - + +
698I PRO* 4.2 14.2 - - + +
701I GLY* 3.5 10.6 - - - -
702I THR* 2.1 44.9 + - - +
703I GLY* 2.5 21.2 + - - +
704I MET* 1.3 77.1 - - - +
706I ARG* 1.3 58.0 + - + +
708I VAL 3.3 1.0 + - - -
709I ALA* 2.9 26.7 + - - +
793I GLU* 4.3 9.0 - - + +
794I LEU* 3.4 40.0 - - + +
1069I ARG* 4.9 3.8 + - - -
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Residues in contact with ARG 706 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I THR* 4.2 16.8 + - - -
7I GLU* 4.4 27.9 - - - +
10I ARG* 4.4 15.0 + - - +
703I GLY 4.4 5.9 + - - +
704I MET 3.4 0.2 - - - -
705I GLU* 1.3 79.3 - - - +
707I ALA* 1.3 59.6 + - - +
710I VAL* 2.9 48.7 + - + +
782I VAL* 4.9 1.6 - - - +
791I LEU 3.2 24.0 + - - -
792I GLY* 3.2 37.3 + - - +
793I GLU* 3.6 28.4 + - + +
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Residues in contact with ALA 707 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL* 4.6 15.9 - - + -
27I LEU* 3.4 6.8 - - - +
703I GLY 4.5 3.9 + - - +
704I MET* 3.1 37.0 + - + +
706I ARG* 1.3 78.1 - - - +
708I VAL* 1.3 58.7 + - - +
711I ASP* 3.1 35.1 - - - +
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Residues in contact with VAL 708 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU* 4.4 4.5 - - + -
520I PRO 4.6 2.5 - - - -
521I LEU* 4.0 16.2 - - + +
524I ILE* 3.8 24.8 - - + +
663I VAL* 4.6 19.1 - - + +
667I LEU* 4.0 20.9 - - + -
704I MET* 2.9 23.1 + - + +
705I GLU 3.7 3.8 - - - +
707I ALA* 1.3 76.1 - - - +
709I ALA* 1.3 69.9 + - - +
710I VAL 3.2 1.2 + - - -
711I ASP 3.3 0.9 + - - -
712I SER* 3.1 25.3 + - - -
794I LEU* 3.6 21.5 - - + -
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Residues in contact with ALA 709 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520I PRO* 5.1 0.4 - - - -
705I GLU 2.9 19.8 + - - +
708I VAL* 1.3 76.0 - - - +
710I VAL* 1.3 60.5 + - - +
712I SER 3.3 9.2 - - - +
714I VAL* 3.4 13.4 - - - +
715I THR* 3.3 17.2 - - - +
789I THR* 3.9 15.9 - - + -
792I GLY* 4.0 11.2 - - - +
793I GLU 3.4 27.8 - - - +
794I LEU* 3.8 6.3 - - - +
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Residues in contact with VAL 710 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706I ARG* 2.9 38.3 + - + +
707I ALA* 5.3 0.2 - - - -
709I ALA* 1.3 76.0 - - - +
711I ASP* 1.3 74.0 + - - +
712I SER 3.0 9.2 - - - +
715I THR* 3.5 9.3 - - + +
717I VAL* 4.3 32.8 - - + +
780I GLY 5.4 3.1 - - - +
782I VAL* 3.8 23.3 - - + -
792I GLY* 3.8 5.4 - - - +
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Residues in contact with ASP 711 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL* 5.1 1.0 - - - +
25I PRO 3.4 11.8 - - - +
26I TYR* 3.5 35.1 + - + -
27I LEU* 3.1 28.2 + - + +
28I LEU* 3.8 5.8 - - - +
524I ILE* 3.7 15.0 - - + -
707I ALA* 3.1 24.6 + - - +
708I VAL 3.3 1.2 + - - -
710I VAL* 1.3 83.9 - - - +
712I SER* 1.3 62.7 + - - +
713I GLY* 3.7 1.2 + - - -
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Residues in contact with SER 712 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LEU* 4.1 6.3 - - - -
520I PRO* 3.9 16.6 + - - -
523I GLU* 3.4 23.6 + - - +
524I ILE* 3.6 16.9 - - - +
527I LYS* 4.4 2.6 + - - -
708I VAL 3.1 16.8 + - - -
709I ALA 3.3 8.0 - - - +
710I VAL 3.0 14.2 - - - +
711I ASP* 1.3 77.3 - - - +
713I GLY* 1.3 60.3 + - - +
714I VAL* 2.9 24.4 + - - +
715I THR* 3.8 2.6 + - - +
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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