Contacts of the strand formed by residues 888 - 891 (chain D) in PDB entry 3N1Q
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 TRP 888 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836C GLU* 3.2 40.9 + - - +
837C ALA 3.6 6.1 - - - -
838C VAL* 3.5 48.4 - - + +
844C MET* 4.8 8.5 - - + -
924C LYS* 4.2 7.0 - - - -
844D MET* 3.4 35.0 - - + -
845D LEU 3.3 11.9 - - - +
846D LYS* 4.1 14.8 - - + -
847D TRP* 3.6 4.5 - - - -
886D LYS* 3.0 44.1 - - - +
887D GLN* 1.3 88.5 - - + +
889D HIS* 1.3 62.2 + - - +
890D MET* 4.4 14.6 - - + -
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Residues in contact with HIS 889 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844D MET* 3.3 9.5 - - - +
845D LEU* 3.0 40.8 + - + +
847D TRP* 3.5 21.5 - - + -
864D ILE* 4.5 11.7 - - + -
880D ASP* 3.2 27.6 + - + +
881D VAL 5.5 0.4 - - - -
882D VAL* 3.3 28.1 - - + +
886D LYS* 4.6 7.1 - - - +
888D TRP* 1.3 77.0 - - - +
890D MET* 1.3 89.2 + - - +
891D ILE* 3.7 15.9 + - + -
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Residues in contact with MET 890 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838C VAL* 4.5 8.7 - - + +
842C GLN* 4.3 13.9 - - - +
890C MET* 4.2 14.8 - - + -
838D VAL* 3.6 33.9 - - + -
842D GLN* 4.2 20.0 - - + +
843D ILE 3.8 3.8 - - - +
844D MET* 3.5 24.2 - - + -
880D ASP* 4.9 0.3 - - - +
886D LYS* 5.6 0.6 - - - +
888D TRP* 4.3 9.6 - - + -
889D HIS* 1.3 93.4 + - - +
891D ILE* 1.3 65.5 + - - +
892D GLY* 3.6 3.1 + - - +
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Residues in contact with ILE 891 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841D THR 3.7 0.7 - - - +
842D GLN* 3.0 9.2 - - - +
843D ILE* 2.8 46.8 + - + +
845D LEU* 3.8 17.0 - - + -
864D ILE* 4.0 16.6 - - + -
866D TYR* 3.9 46.2 - - + -
880D ASP* 4.5 1.8 - - - +
889D HIS* 3.7 20.2 - - + +
890D MET* 1.3 72.3 - - - +
892D GLY* 1.3 61.8 + - - +
894D LEU* 4.0 17.4 - - + +
902D ILE* 4.1 24.7 - - + -
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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