Contacts of the strand formed by residues 58 - 66 (chain A) in PDB entry 5U2H
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 ILE 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 5.5 5.2 - - + +
57A LEU* 1.3 78.1 - - - +
59A SER* 1.3 64.2 + - - +
195A ASN 3.8 0.7 - - - +
196A ILE* 3.8 0.2 - - - -
197A ASP* 2.9 50.4 + - + +
199A PRO* 4.7 20.2 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.8 7.7 + - - +
58A ILE* 1.3 80.4 - - - +
60A SER* 1.3 61.1 + - - +
61A VAL* 4.6 3.6 - - - +
100A ASN* 4.1 13.4 + - - -
194A ASN* 5.5 2.7 - - - -
195A ASN 3.2 11.9 - - - -
196A ILE* 5.3 0.2 - - - -
321A VAL* 3.0 50.6 + - - +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 1.3 73.9 - - - +
61A VAL* 1.3 65.4 + - - +
100A ASN* 4.7 2.7 - - - +
193A LYS 3.9 1.2 - - - +
194A ASN* 3.7 0.7 - - - -
195A ASN* 2.9 43.0 + - - +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 4.6 1.6 - - - +
60A SER* 1.3 80.7 + - - +
62A HIS* 1.3 66.7 + - - +
63A THR* 4.1 5.8 - - + -
97A LEU* 3.2 22.3 - - + +
100A ASN* 4.1 24.5 + - + +
192A ILE* 5.0 2.2 - - + -
193A LYS 3.4 14.1 - - - +
194A ASN* 4.4 10.3 - - + -
319A ILE* 3.4 51.4 - - + -
321A VAL* 4.0 17.9 - - + -
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 1.3 75.3 - - - +
63A THR* 1.3 87.0 + - - +
64A LYS* 4.8 8.7 - - + +
97A LEU* 4.1 5.8 - - - +
191A LEU 3.8 0.9 - - - +
192A ILE* 3.7 1.2 - - - -
193A LYS* 2.9 45.4 + - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.1 2.0 - - + -
62A HIS* 1.3 97.7 + - - +
64A LYS* 1.3 61.1 + - - +
65A VAL* 4.3 3.6 - - - +
97A LEU* 3.2 33.1 + - + +
102A PHE* 3.6 28.4 - - + +
190A VAL* 4.7 2.9 - - + -
191A LEU 3.2 8.7 - - - +
192A ILE* 4.6 3.4 - - + -
319A ILE* 3.2 34.3 - - + -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 4.8 11.2 - - + +
63A THR* 1.3 73.6 - - - +
65A VAL* 1.3 66.5 + - - +
66A LYS* 3.8 1.7 + - - +
189A THR 4.4 0.2 - - - +
190A VAL* 3.7 2.5 - - - -
191A LEU* 2.9 44.1 + - + +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 5.6 2.7 - - - +
64A LYS* 1.3 75.9 - - - +
66A LYS* 1.3 65.5 + - - +
90A THR* 3.6 26.7 + - + +
93A TYR* 3.4 35.0 - - + +
94A THR* 3.5 26.0 - - + +
95A PHE 5.7 0.2 - - - +
102A PHE* 4.7 19.7 - - + -
104A VAL* 4.9 8.7 - - + -
188A PHE* 5.2 6.1 - - + -
189A THR 4.3 2.5 - - - +
190A VAL* 4.7 11.2 - - + +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS 4.8 2.9 - - - +
65A VAL* 1.3 76.7 - - - +
67A GLY* 1.3 61.3 + - - +
90A THR* 5.0 1.1 - - - -
93A TYR* 4.0 1.3 - - - -
188A PHE* 3.5 7.6 - - - +
189A THR* 2.9 55.8 + - - +
191A LEU* 5.8 1.8 - - + +
228A ILE* 6.0 0.4 - - + -
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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