Contacts of the strand formed by residues 648 - 651 (chain A) in PDB entry 4X8G
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 ASN 648 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A VAL* 3.8 2.8 - - - +
309A TYR* 2.8 46.9 + - + +
349A GLN* 2.8 37.9 + - + -
352A MET* 3.4 38.0 + - + +
353A GLU* 5.5 0.9 - - - -
354A ILE* 4.3 11.2 + - + +
590A LEU* 5.3 0.2 - - - -
646A GLY 4.0 0.2 + - - -
647A THR* 1.3 77.2 - - - +
649A VAL* 1.3 82.2 + - - +
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Residues in contact with VAL 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO* 3.8 15.7 - - + -
307A GLU 3.5 11.4 - - - +
308A VAL* 4.3 3.1 - - + -
309A TYR* 4.8 0.4 - - - -
354A ILE* 3.4 21.7 + - - +
590A LEU* 3.6 27.6 - - + -
592A LEU* 3.7 23.3 - - + -
648A ASN* 1.3 90.2 + - - +
650A ARG* 1.3 65.4 + - - +
651A ARG* 3.6 34.0 + - - +
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Residues in contact with ARG 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO* 3.4 3.1 - - - +
306A GLN* 2.5 77.3 + - - +
307A GLU* 2.7 52.9 + - - +
309A TYR* 3.5 22.9 + - + -
333A LYS* 5.7 2.6 - - - +
354A ILE* 4.1 18.6 - - + -
365A PRO* 4.2 20.8 - - + +
389A PHE* 4.2 18.0 - - - -
649A VAL* 1.3 73.7 - - - +
651A ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 3.8 32.9 + - - +
300A PRO 3.2 25.6 + - - -
301A ASN* 2.9 40.2 + - - +
303A GLN* 3.2 13.8 + - + +
304A PRO 3.2 13.7 - - - +
305A PRO* 3.7 12.5 - - + +
306A GLN* 3.7 9.9 - - - +
354A ILE* 5.6 1.4 + - - +
591A VAL 2.6 30.5 + - - +
592A LEU* 4.7 0.6 - - - +
593A GLY 5.2 0.2 - - - +
649A VAL* 3.6 34.1 + - + +
650A ARG* 1.3 79.2 - - - +
652A LYS* 1.3 64.7 + - - +
653A PRO* 3.4 8.8 - - - +
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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
------------------------------------------------------------
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