Contacts of the strand formed by residues 418 - 422 (chain q) in PDB entry 6FF7
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 VAL 418 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416q HIS* 3.7 14.4 - - - +
417q GLN* 1.3 83.4 - - + +
419q LEU* 1.3 63.3 + - - +
549q VAL* 3.2 13.9 - - + +
565q PHE* 4.9 12.6 - - + +
568q ALA* 3.3 25.9 - - + +
569q PRO 4.3 1.4 - - - -
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Residues in contact with LEU 419 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412q ALA* 5.1 21.5 - - + +
413q ILE* 5.6 3.8 - - - +
416q HIS* 5.3 4.0 - - + +
418q VAL* 1.3 77.2 - - - +
420q ILE* 1.3 65.6 + - - +
549q VAL 3.0 8.5 + - - +
550q LEU* 3.4 7.0 - - + -
551q VAL* 2.8 26.3 + - - +
568q ALA* 4.3 3.6 - - - -
569q PRO* 3.8 11.7 - - + +
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Residues in contact with ILE 420 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419q LEU* 1.3 78.2 - - - +
421q ILE* 1.3 62.0 + - - +
551q VAL* 3.2 14.6 - - + +
558q THR* 5.8 5.4 - - - +
561q PHE* 5.0 15.9 - - + -
562q SER* 5.6 6.7 - - - +
565q PHE* 6.5 0.2 - - + -
568q ALA* 4.8 3.8 - - + +
569q PRO 3.0 13.7 + - - +
570q VAL* 3.4 9.9 - - + +
571q PHE* 3.0 26.0 + - - +
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Residues in contact with ILE 421 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419q LEU 4.2 0.2 - - - -
420q ILE* 1.3 74.8 - - - +
422q GLU* 1.3 61.6 + - - +
429q LYS* 6.3 2.9 - - + -
550q LEU* 5.9 5.4 - - + +
551q VAL 2.7 13.3 + - - +
552q ALA* 3.2 11.4 - - + +
553q SER 2.9 24.8 + - - -
571q PHE* 3.4 13.5 - - + +
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Residues in contact with GLU 422 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420q ILE* 4.2 0.6 - - + -
421q ILE* 1.3 76.7 - - - +
423q GLY* 1.3 59.5 + - - +
553q SER* 3.1 13.2 - - - +
555q THR 3.6 20.9 - - - +
556q MET* 4.6 10.3 - - - +
557q ASP 5.6 1.1 - - - +
558q THR* 6.0 3.8 - - - -
571q PHE 2.9 11.0 + - - +
572q ARG* 3.4 9.0 - - + -
573q ILE* 2.9 26.9 + - - +
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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