Contacts of the strand formed by residues 52 - 57 (chain d) 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 GLY 52 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48d MET* 3.0 18.6 - - - -
49d ALA 3.3 8.4 + - - +
50d THR 2.7 11.5 + - - -
51d SER* 1.3 76.9 - - - +
53d GLN* 1.3 63.8 + - - -
54d GLN* 2.9 11.7 + - - +
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Residues in contact with GLN 53 (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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46d VAL* 6.0 5.2 - - + -
47d GLU 4.3 2.0 - - - -
48d MET* 4.1 9.8 - - + +
52d GLY* 1.3 69.3 - - - -
54d GLN* 1.3 60.9 + - - +
55d ASN 3.8 4.7 - - - +
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Residues in contact with GLN 54 (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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47d GLU 3.1 9.1 + - - +
49d ALA* 4.5 15.3 - - + +
52d GLY 2.9 11.9 + - - +
53d GLN* 1.3 74.3 - - - +
55d ASN* 1.3 62.1 + - + +
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Residues in contact with ASN 55 (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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46d VAL* 3.7 6.9 - - - +
47d GLU* 3.1 36.9 + - + +
53d GLN* 5.1 3.3 - - - +
54d GLN* 1.3 81.5 + - + +
56d ASN* 1.3 65.6 + - - +
57d ILE* 6.5 0.2 - - + -
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Residues in contact with ASN 56 (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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91c SER* 5.0 5.4 - - - -
92c ASN 5.9 0.3 + - - -
45d CYS 3.3 10.5 - - - +
46d VAL* 4.3 4.9 - - + +
55d ASN* 1.3 81.1 - - - +
57d ILE* 1.3 61.6 + - - +
58d GLY 4.3 0.3 + - - -
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Residues in contact with ILE 57 (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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88c GLN* 4.2 24.7 - - + -
91c SER* 4.3 14.8 - - - +
42d ILE 5.5 0.2 - - - +
44d GLU* 3.5 1.4 - - - -
45d CYS* 2.8 45.7 + - + +
55d ASN* 6.5 0.2 - - + -
56d ASN* 1.3 75.0 - - - +
58d GLY* 1.3 63.3 + - - +
59d MET* 4.3 6.7 - - - +
60d VAL* 5.2 5.4 - - + -
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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