Contacts of the helix formed by residues 639 - 644 (chain J) in PDB entry 1O1F
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 639 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237 GLY 2.4 26.0 - - - +
247 ASP 2.8 6.8 - - - +
3417 ILE* 4.9 1.0 - - - +
3447 SER* 2.4 39.2 + - - -
3457 ILE* 1.9 19.0 - - - +
3487 SER* 3.0 4.5 - - - -
541J MET* 5.3 0.2 - - - -
632J GLY 3.1 0.7 - - - +
633J GLY* 4.0 4.0 - - - -
638J GLY* 1.3 62.1 - - - -
640J LYS* 1.3 55.3 + - - -
641J LYS 3.1 3.1 - - - -
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Residues in contact with LYS 640 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237 GLY 2.1 24.2 - - - +
3457 ILE* 6.0 1.1 - - + -
3487 SER* 3.6 3.0 + - - -
540J CYS 6.1 0.7 - - - -
600J MLY 3.2 39.2 + - - +
601J ASP 5.0 2.2 + - - -
602J PRO* 5.5 2.4 - - - +
629J GLU 4.1 0.9 - - - +
633J GLY* 4.8 7.6 - - - -
638J GLY 4.3 1.5 - - - +
639J GLY* 1.3 66.7 - - - -
641J LYS* 1.4 53.5 + - - +
643J GLY* 3.4 2.9 + - - -
644J SER 3.6 0.2 + - - -
645J SER* 2.1 60.8 + - - +
646J PHE 2.9 21.3 + - - +
647J GLN* 4.1 9.0 + - + +
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Residues in contact with LYS 641 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 GLU* 3.3 55.2 - - + +
57 THR* 5.0 6.6 - - - +
217 PHE* 5.1 0.7 - - - +
227 ALA 2.6 13.9 - - - +
237 GLY* 1.6 14.9 - - - -
3477 ALA 4.7 1.2 + - - -
3487 SER* 1.8 33.0 + - - +
3497 LEU 4.0 8.1 + - - -
3507 SER* 4.3 3.6 - - - +
537J GLU* 5.1 1.8 + - - -
640J LYS* 1.4 70.1 - - - +
642J LYS* 1.2 51.0 + - - -
643J GLY 3.0 3.4 - - - -
644J SER* 2.9 20.7 + - - +
645J SER 3.2 12.8 - - - +
647J GLN* 1.8 77.8 - - + +
651J ALA* 5.0 10.0 - - - +
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Residues in contact with LYS 642 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97 VAL* 4.3 1.1 - - - -
217 PHE* 2.2 31.2 - - - +
227 ALA* 2.7 6.7 - - - +
237 GLY* 1.0 102.4 - - - +
247 ASP* 1.0 191.1 - - + +
287 ARG* 3.5 4.3 + - - -
3407 TRP* 2.5 48.6 + - + -
3417 ILE* 2.9 8.7 + - - +
3447 SER* 0.8 207.1 - - - +
641J LYS 1.2 34.7 - - - -
643J GLY* 1.3 45.6 - - - -
644J SER 3.6 0.2 - - - -
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Residues in contact with GLY 643 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237 GLY 2.5 6.3 - - - -
247 ASP* 2.2 21.5 - - - +
287 ARG* 5.2 0.7 - - - -
628J GLY 3.0 5.3 - - - +
629J GLU* 1.9 39.8 + - - -
631J GLU* 4.9 2.0 - - - -
632J GLY* 3.4 3.8 - - - -
642J LYS* 1.3 65.4 - - - +
644J SER* 1.3 73.3 + - - +
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Residues in contact with SER 644 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 GLU* 5.0 10.1 - - - +
57 THR* 6.1 4.5 - - - -
625J THR 4.0 0.7 + - - -
628J GLY 3.5 2.9 + - - -
629J GLU* 0.7 138.7 + - - +
641J LYS* 2.9 14.8 + - - +
643J GLY* 1.3 80.5 + - - +
645J SER* 1.3 53.1 - - - +
646J PHE* 4.0 1.0 + - - -
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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