Contacts of the strand formed by residues 51 - 55 (chain h) 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 LYS 51 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3289 TYR* 2.9 29.2 - - + +
3319 VAL* 1.8 57.2 - - + +
3329 GLU 3.5 0.9 - - - +
44h ILE 3.1 11.0 - - - +
45h ASN* 4.6 4.3 - - + +
46h CYS* 5.4 0.4 - - - -
50h LYS* 1.3 75.3 - - - +
52h LEU* 1.3 50.5 + - - +
72h GLU* 3.3 4.0 - - - +
73h MET 2.8 15.2 + - - +
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Residues in contact with LEU 52 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3319 VAL 1.1 38.0 + - - -
3329 GLU* 0.8 131.5 - - - +
3349 LEU* 4.3 0.2 - - - -
3359 GLY* 1.7 55.0 - - - +
3369 GLU 3.3 0.4 - - - +
44h ILE* 2.7 12.6 + - + +
46h CYS* 5.2 4.0 - - + +
51h LYS* 1.3 65.0 - - - +
53h LEU 1.3 26.2 - - - +
72h GLU* 4.5 2.5 - - + +
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Residues in contact with LEU 53 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3299 GLU 2.2 15.5 - - - +
3309 TYR* 1.3 65.6 - - - +
3319 VAL 1.9 11.9 + - - -
3339 ILE* 0.9 209.8 - - + +
3349 LEU 1.7 20.0 + - - +
52h LEU 1.3 57.0 - - - -
54h GLY* 1.3 5.9 - - - -
69h ASN 3.4 1.9 - - - +
70h VAL* 3.3 0.5 - - - -
71h LYS* 2.7 13.6 + - + +
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Residues in contact with GLY 54 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3339 ILE* 1.1 101.7 - - - +
3369 GLU* 4.1 4.7 - - - +
41h GLN* 3.2 7.4 - - - -
42h VAL* 2.8 28.3 + - - +
53h LEU 1.3 13.7 - - - -
55h ARG* 1.3 60.4 + - - -
68h GLU 3.7 6.7 - - - -
69h ASN* 3.9 4.5 - - - -
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Residues in contact with ARG 55 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3339 ILE 3.9 0.2 + - - -
3369 GLU* 4.3 2.9 - - - -
3379 GLN 3.6 1.4 + - - -
39h ASN* 4.8 11.9 - - + +
40h THR 3.9 15.3 - - - +
41h GLN* 5.1 0.9 - - - -
54h GLY* 1.3 74.6 - - - -
56h VAL* 1.3 61.2 + - - +
57h LYS 3.8 0.2 - - - -
67h LEU* 3.3 7.3 - - - -
68h GLU* 3.0 44.2 + - + +
69h ASN* 5.4 2.9 - - + +
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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