Contacts of the helix formed by residues 703 - 713 (chain C) in PDB entry 4YLP
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 703 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C ARG* 4.2 19.4 - - - +
14C ASP* 6.4 1.6 - - - -
701C GLY 3.5 2.4 - - - -
702C THR* 1.3 75.6 - - - +
704C MET* 1.3 58.9 + - - +
705C GLU* 3.0 11.1 + - - -
706C ARG* 3.4 24.5 + - - +
707C ALA* 4.4 1.2 + - - +
793C GLU* 5.8 0.7 - - - -
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Residues in contact with MET 704 (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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20C GLN* 5.5 2.0 - - - +
24C VAL* 4.6 31.0 - - + -
27C LEU* 6.1 0.9 - - + -
577C VAL* 4.4 16.6 - - + -
578C TYR* 6.4 0.7 - - - -
658C GLN* 3.4 35.0 - - + +
663C VAL* 4.8 11.4 - - + -
666C SER* 3.3 28.0 - - - +
667C LEU* 3.4 11.7 - - + -
702C THR* 3.0 20.5 + - - +
703C GLY* 1.3 78.3 - - - +
705C GLU* 1.3 55.8 + - - +
706C ARG 3.2 0.4 - - - -
707C ALA* 3.2 14.0 + - + +
708C VAL* 3.0 30.6 + - + +
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Residues in contact with GLU 705 (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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12C ARG* 5.7 3.3 + - - +
667C LEU* 2.9 37.5 - - + +
698C PRO* 4.5 11.4 - - + -
701C GLY* 4.2 7.4 - - - -
702C THR* 3.1 24.3 + - - -
703C GLY* 3.0 3.9 + - - -
704C MET* 1.3 80.0 + - - +
706C ARG* 1.3 63.1 + - - +
708C VAL* 4.4 2.5 - - - -
709C ALA* 3.1 15.6 + - - +
793C GLU* 4.0 13.7 - - + -
794C LEU* 2.9 54.9 + - + +
796C LEU* 6.1 2.3 - - + +
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Residues in contact with ARG 706 (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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6C THR* 5.0 5.8 + - - -
7C GLU* 4.5 30.5 - - - +
10C ARG* 3.2 26.6 + - - +
12C ARG* 5.4 6.1 - - - +
703C GLY* 3.4 15.8 + - - +
705C GLU* 1.3 77.5 - - - +
707C ALA* 1.3 57.8 + - - +
709C ALA* 3.4 2.3 + - - +
710C VAL* 2.6 44.1 + - + +
791C LEU 4.2 10.9 + - - -
792C GLY* 3.5 22.3 - - - +
793C GLU* 3.2 33.0 + - + +
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Residues in contact with ALA 707 (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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24C VAL* 5.0 24.0 - - + +
27C LEU* 5.6 4.9 - - + -
703C GLY 4.4 1.0 + - - +
704C MET* 3.2 17.6 + - + +
706C ARG* 1.3 76.8 - - - +
708C VAL* 1.3 67.0 + - + +
710C VAL* 3.7 6.0 - - - +
711C ASP* 3.0 36.5 + - - +
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Residues in contact with VAL 708 (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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27C LEU* 5.5 4.0 - - + -
521C LEU* 5.0 4.9 - - + -
524C ILE* 3.2 22.8 - - + +
663C VAL* 4.4 18.6 - - + -
667C LEU* 3.4 31.2 - - + -
704C MET* 3.0 23.6 + - + +
705C GLU 3.8 2.0 - - - +
706C ARG 3.2 0.2 - - - -
707C ALA* 1.3 76.3 - - + +
709C ALA* 1.3 65.1 + - - +
711C ASP* 4.0 2.7 - - - +
712C SER* 3.0 22.2 + - - -
794C LEU* 3.4 33.0 - - + -
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Residues in contact with ALA 709 (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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705C GLU 3.1 10.9 + - - +
706C ARG 3.6 0.4 - - - +
708C VAL* 1.3 82.5 - - - +
710C VAL* 1.3 63.0 + - + +
712C SER* 2.2 25.9 + - - -
713C GLY 3.6 3.1 + - - -
715C THR* 3.9 17.1 + - + +
789C THR* 4.0 18.6 - - + -
792C GLY 3.2 27.1 - - - +
793C GLU 4.0 2.7 - - - -
794C LEU* 4.0 11.2 - - - +
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Residues in contact with VAL 710 (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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26C TYR* 5.0 6.3 + - + -
706C ARG* 2.6 40.1 + - + +
707C ALA* 3.7 7.2 - - - +
708C VAL 3.2 0.2 - - - -
709C ALA* 1.3 78.3 - - + +
711C ASP* 1.3 69.1 + - - +
713C GLY* 3.5 11.1 + - - -
715C THR* 4.3 10.3 + - - -
717C VAL* 4.5 21.0 - - + +
780C GLY 5.9 2.5 - - - +
782C VAL* 5.5 11.2 - - + -
792C GLY 4.6 4.0 - - - +
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Residues in contact with ASP 711 (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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24C VAL 5.6 1.8 - - - +
25C PRO 4.1 0.3 - - - +
26C TYR* 3.2 42.0 + - + -
27C LEU* 2.6 53.6 + - + +
28C LEU* 3.9 14.9 + - - +
524C ILE* 4.8 5.2 - - + -
707C ALA* 3.0 23.3 + - - +
708C VAL 4.1 2.0 - - - +
710C VAL* 1.3 83.7 - - - +
712C SER* 1.3 67.1 + - - +
713C GLY* 2.9 6.2 + - - -
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Residues in contact with SER 712 (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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28C LEU* 4.6 7.3 - - - +
133C ASN* 4.0 13.7 + - - +
520C PRO* 4.1 15.9 - - - +
523C GLU* 4.7 8.3 - - - +
524C ILE* 2.9 38.7 - - - +
527C LYS* 4.7 2.6 + - - -
708C VAL 3.0 9.5 + - - -
709C ALA* 2.2 36.0 + - - -
711C ASP* 1.3 73.8 - - - +
713C GLY* 1.3 59.1 + - - +
714C VAL* 3.1 15.0 + - - +
789C THR* 5.6 0.5 - - - +
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Residues in contact with GLY 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 5.3 4.3 - - - -
133C ASN* 3.4 23.1 + - - +
709C ALA 3.6 1.0 + - - -
710C VAL 3.5 12.1 + - - -
711C ASP 2.9 6.8 + - - -
712C SER* 1.3 81.1 + - - +
714C VAL* 1.3 61.8 + - - +
715C THR* 3.3 12.9 - - - +
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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