Contacts of the strand formed by residues 427 - 431 (chain B) in PDB entry 4N7F
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 427 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A VAL* 5.3 2.4 - - - +
431A HIS* 4.2 13.5 - - - -
423B LEU* 4.1 18.5 - - + +
424B PRO* 3.2 34.4 + - + +
425B LYS 3.5 10.1 - - - -
426B GLY* 1.3 81.4 - - - +
428B GLU* 1.3 68.3 + - - +
439B PHE* 3.8 13.5 - - + -
440B ILE 3.2 18.2 - - - -
441B ASP* 3.5 41.4 + - + -
443B ASN* 4.1 3.6 - - - +
446B THR* 4.9 5.6 - - + -
448B THR* 3.8 29.6 - - + -
450B GLU 5.0 0.7 - - - -
452B PRO* 3.6 35.6 - - + +
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Residues in contact with GLU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.7 19.3 - - - +
428A GLU* 5.7 1.7 - - - +
429A VAL* 4.3 30.0 + - + +
453A ARG* 5.1 2.8 + - - +
423B LEU* 3.6 10.1 - - - -
427B TRP* 1.3 78.8 - - - +
429B VAL* 1.3 67.5 + - - +
430B ARG* 4.3 9.2 + - - -
439B PHE* 3.3 6.9 - - - +
440B ILE* 2.9 48.1 + - + +
442B HIS* 2.7 34.0 + - + +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A MET* 6.2 2.2 - - + -
422A PHE* 5.9 0.5 - - - -
423A LEU 5.9 0.2 + - - -
453A ARG* 3.4 31.8 + - - +
2B MET* 4.9 6.7 - - + -
423B LEU* 3.5 10.8 - - + +
428B GLU* 1.3 79.7 - - - +
430B ARG* 1.3 73.4 + - - +
431B HIS* 4.3 15.5 - - + -
437B PRO* 4.1 15.5 - - + -
438B PHE 3.3 12.8 - - - +
439B PHE* 3.7 22.4 - - + -
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Residues in contact with ARG 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER 3.8 12.8 - - - +
422A PHE* 5.2 7.9 - - + +
428B GLU* 4.3 9.9 + - - -
429B VAL* 1.3 77.5 + - - +
431B HIS* 1.3 69.5 + - - +
437B PRO* 3.4 3.6 - - - +
438B PHE* 2.8 68.7 + - + +
440B ILE* 3.6 40.2 - - + +
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Residues in contact with HIS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A MET* 3.5 32.5 - - + +
3A GLY 4.4 3.3 + - - -
4A SER* 3.1 43.9 + - - +
2B MET* 5.4 4.3 - - + +
429B VAL* 4.3 20.0 - - + -
430B ARG* 1.3 84.1 - - - +
432B ALA* 1.3 66.3 + - - +
433B PRO* 4.8 0.2 - - - +
435B GLY* 3.4 25.4 - - - -
436B ARG 3.4 4.3 - - - +
437B PRO* 3.6 22.2 - - + +
438B PHE* 4.0 5.7 - - - -
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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