Contacts of the helix formed by residues 623 - 634 (chain F) in PDB entry 4G5O
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 623 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B GLU* 5.3 5.4 - - - +
622F GLU* 1.3 74.1 - - - +
624F PHE* 1.3 65.9 + - - +
625F PHE* 2.7 42.7 + - - +
626F SER* 3.1 26.3 + - - +
627F LEU* 3.5 20.6 + - - +
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Residues in contact with PHE 624 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.1 1.3 - - + -
215B PHE* 3.8 35.7 - + - -
252B SER* 3.8 21.8 - - - -
253B ILE* 3.8 31.2 - - + -
256B ASN* 3.3 26.0 - - - +
258B TRP* 4.3 8.5 - + + -
259B PHE* 3.6 23.1 - + - -
622F GLU 3.8 2.4 + - - -
623F ASP* 1.3 77.9 + - - +
625F PHE* 1.3 82.5 + + + +
627F LEU* 3.6 6.7 + - - +
628F ILE* 3.3 33.6 + - + +
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Residues in contact with PHE 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLU* 3.6 26.5 - - - +
211B TRP* 3.1 34.2 - + + -
212B ILE* 4.4 18.6 - - + -
215B PHE* 3.3 49.6 - + + -
258B TRP* 3.3 40.6 - + - -
623F ASP* 2.7 18.6 + - - +
624F PHE* 1.3 80.0 - + + +
626F SER* 1.3 64.2 + - - +
628F ILE* 3.1 6.8 + - + +
629F LEU* 3.0 24.5 + - - +
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Residues in contact with SER 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLU* 5.6 0.6 + - - -
622F GLU* 5.8 0.4 - - - -
623F ASP* 3.1 33.1 + - - +
625F PHE* 1.3 76.0 - - - +
627F LEU* 1.3 64.8 + - - +
629F LEU* 3.0 23.3 + - - +
630F ARG* 3.1 35.5 + - - +
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Residues in contact with LEU 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLU 6.0 0.4 - - - +
248B LYS* 4.2 39.3 - - + +
249B LEU* 3.5 15.1 - - + +
252B SER* 4.4 21.1 - - - +
622F GLU* 4.4 17.3 - - + -
623F ASP 3.5 6.9 + - - +
624F PHE* 3.7 10.8 - - - +
625F PHE 3.3 0.2 - - - -
626F SER* 1.3 79.7 - - - +
628F ILE* 1.3 56.6 + - - +
630F ARG* 3.3 34.2 + - - +
631F SER* 2.6 38.6 + - - +
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Residues in contact with ILE 628 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.2 11.9 - - + -
201B VAL* 4.7 0.2 - - + -
211B TRP* 4.1 19.7 - - + -
215B PHE* 4.4 4.7 - - + -
249B LEU* 3.9 24.9 - - + -
252B SER* 4.9 2.0 - - - +
253B ILE* 4.2 13.9 - - + -
624F PHE* 3.3 45.3 - - + +
625F PHE* 3.1 9.5 + - - +
627F LEU* 1.3 78.4 - - + +
629F LEU* 1.3 63.6 + - - +
631F SER* 3.9 0.5 - - - -
632F GLN* 3.0 54.8 + - + +
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Residues in contact with LEU 629 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLY 5.0 2.3 - - - +
203B GLY* 4.0 26.3 - - - +
206B SER 4.3 17.3 - - - +
207B GLU* 4.0 32.3 - - + +
211B TRP* 3.6 34.5 - - + +
625F PHE 3.0 16.3 + - - +
626F SER* 3.0 11.9 + - - +
628F ILE* 1.3 76.4 - - - +
630F ARG* 1.3 64.9 + - + +
632F GLN* 4.0 1.8 - - - +
633F ALA* 3.2 25.3 + - - +
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Residues in contact with ARG 630 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLU* 4.4 15.4 + - - -
248B LYS* 5.4 3.0 - - - +
622F GLU* 4.9 10.3 - - - +
626F SER* 3.1 27.2 + - - +
627F LEU* 3.3 41.9 - - - +
629F LEU* 1.3 76.9 - - + +
631F SER* 1.3 63.7 + - - +
633F ALA* 3.3 12.4 + - - +
634F LYS* 3.1 21.7 - - + +
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Residues in contact with SER 631 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 3.8 7.4 - - - -
42B GLY 2.9 18.8 + - - -
242B ARG* 3.9 4.1 + - - +
245B GLU* 5.4 11.2 + - - +
249B LEU* 3.3 31.7 - - - +
627F LEU* 2.6 30.0 + - - +
628F ILE 3.3 1.8 + - - -
630F ARG* 1.3 77.3 - - - +
632F GLN* 1.3 60.6 + - - +
633F ALA 3.5 0.2 + - - -
634F LYS* 3.5 21.6 + - - +
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Residues in contact with GLN 632 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU 4.6 1.0 - - - +
39B LEU* 3.5 14.4 - - - +
40B GLY 2.7 44.7 - - - +
41B ALA* 4.5 0.2 - - - -
42B GLY* 3.7 13.9 - - - +
46B LYS* 3.7 18.3 + - - +
200B ASP* 4.7 0.2 - - - +
201B VAL* 3.6 20.8 - - - +
202B GLY* 3.5 26.3 + - - +
249B LEU* 4.5 2.2 - - - +
628F ILE* 3.0 43.6 + - - +
629F LEU 4.4 0.2 - - - +
631F SER* 1.3 76.9 - - - +
633F ALA* 1.3 62.8 - - - +
634F LYS 3.3 0.4 - - - -
635F ARG* 4.0 12.5 + - - +
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Residues in contact with ALA 633 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLY 4.8 0.2 + - - -
203B GLY* 5.1 11.4 - - - +
629F LEU 3.2 19.9 + - - +
630F ARG* 3.4 8.5 - - - +
631F SER 3.2 0.2 - - - -
632F GLN* 1.3 75.8 - - - +
634F LYS* 1.3 55.1 + - + +
635F ARG* 2.6 22.5 + - - +
637F ASP* 5.4 5.5 - - - +
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Residues in contact with LYS 634 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY* 3.5 19.0 - - - +
43B GLU* 4.3 1.4 - - - +
237B ASP* 5.0 10.8 + - - -
238B GLU* 3.3 33.5 + - - +
242B ARG* 4.0 23.3 + - - +
245B GLU* 3.4 23.1 + - - +
630F ARG* 3.1 21.1 - - + +
631F SER* 3.5 11.4 + - - +
632F GLN 3.3 1.6 - - - -
633F ALA* 1.3 75.7 - - + +
635F ARG* 1.3 66.7 + - - +
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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