Contacts of the strand formed by residues 55 - 60 (chain f) in PDB entry 5W97
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 55 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507a GLU* 3.6 1.6 - - - +
9d GLU* 3.3 44.9 + - - +
11d TYR* 4.5 5.9 + - - -
12d ALA* 3.6 22.7 - - + -
51f SER* 3.3 5.0 + - - -
53f THR* 3.3 26.8 - - + +
54f ASN* 1.3 95.3 + - - +
56f ARG* 1.3 61.7 + - - +
73f TRP* 3.8 28.3 - - + -
74f LEU 3.1 14.4 - - - +
75f HIS* 3.8 28.3 - - + +
91f LEU* 3.9 3.3 - - - +
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Residues in contact with ARG 56 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507a GLU* 3.7 21.0 + - + +
508a PRO 2.8 22.3 + - - +
509a THR 3.0 24.0 + - - -
510a TYR* 3.8 28.3 - - - +
32f ASN* 3.2 37.8 + - - +
49f VAL* 3.7 9.4 - - + -
50f PRO* 2.8 44.3 + - - +
51f SER* 3.8 6.7 - - - +
55f LYS* 1.3 76.8 - - - +
57f ILE* 1.3 69.2 + - - +
58f VAL* 3.9 0.7 - - - +
73f TRP* 3.8 9.3 - - - -
74f LEU* 2.9 35.9 + - - +
91f LEU* 3.9 12.3 - - + +
95f GLN* 4.8 0.6 - - - +
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Residues in contact with ILE 57 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492a LEU* 4.2 13.2 - - + -
495a LEU* 4.2 15.7 - - + -
496a ASN* 4.3 8.1 - - - +
505a PHE* 3.8 27.6 - - + -
508a PRO 5.3 0.2 + - - -
509a THR* 3.4 23.5 - - + -
510a TYR* 2.9 26.7 + - - +
56f ARG* 1.3 73.8 - - - +
58f VAL* 1.3 70.3 + - - +
71f TRP* 3.8 11.9 - - + -
72f PHE 3.6 6.1 - - - +
73f TRP* 3.7 43.6 - - + +
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Residues in contact with VAL 58 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510a TYR* 3.4 13.5 - - + +
49f VAL* 4.2 12.3 - - + -
56f ARG 3.9 0.9 - - - +
57f ILE* 1.3 76.8 - - - +
59f GLY* 1.3 73.2 + - - +
70f ILE 3.6 1.2 - - - +
71f TRP* 3.2 4.4 - - - -
72f PHE* 2.7 62.8 + - + +
74f LEU* 3.8 37.2 - - + -
89f TYR* 3.7 28.7 - - + -
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Residues in contact with GLY 59 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510a TYR 2.9 19.1 + - - +
511a VAL* 3.5 15.5 - - - +
512a ASN 4.4 1.9 + - - -
57f ILE 4.2 0.2 + - - -
58f VAL* 1.3 77.2 - - - +
60f CYS* 1.3 61.5 + - - -
69f VAL* 3.5 9.2 - - - -
70f ILE 3.2 4.3 - - - -
71f TRP* 3.1 31.5 - - - -
89f TYR* 4.7 0.7 + - - -
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Residues in contact with CYS 60 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512a ASN* 5.9 0.9 - - - +
514a LYS* 3.7 9.6 - - - +
59f GLY* 1.3 73.9 - - - -
61f ILE* 1.3 62.6 + - - +
62f CYS* 3.5 5.9 + - - -
68f THR 4.4 0.7 - - - +
69f VAL* 3.6 3.3 - - - +
70f ILE* 2.7 38.2 + - - +
72f PHE* 4.3 8.7 - - + -
82f CYS* 3.8 9.4 - - - -
87f THR* 3.6 11.2 - - - -
89f TYR* 3.1 26.5 - - + +
101f ZN 2.3 36.8 - - - -
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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
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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