Contacts of the strand formed by residues 81 - 90 (chain U) in PDB entry 1W13
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 MET 81 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67U TYR* 3.4 7.7 - - - -
68U LEU 2.9 32.0 + - - +
79U GLY 3.9 4.7 - - - +
80U GLU* 1.3 90.4 - - - +
82U LYS* 1.3 60.6 + - - +
83U PHE* 3.5 30.6 - - + -
113U GLN* 5.5 16.6 - - + +
118U ILE* 3.7 22.0 - - + -
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Residues in contact with LYS 82 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36U ARG* 4.7 10.9 - - - +
65U ILE* 3.9 38.9 - - + +
66U VAL 3.7 3.4 - - - -
67U TYR* 3.6 31.2 + - + +
81U MET* 1.3 73.0 - - - +
83U PHE* 1.3 73.5 + - - +
84U GLU* 5.4 2.5 - - - +
110U SER* 4.1 31.9 + - - +
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Residues in contact with PHE 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65U ILE* 3.6 9.2 - - - +
66U VAL* 2.8 38.0 + - + +
68U LEU* 3.6 26.0 - - + -
81U MET* 3.5 40.8 - - + -
82U LYS* 1.3 78.7 - - - +
84U GLU* 1.3 63.6 + - - +
108U ILE* 3.8 27.8 - - + -
109U ARG* 3.6 9.2 - - - +
110U SER* 3.5 32.8 - - + +
111U CYS 3.8 7.6 - - - -
112U ALA* 3.6 38.4 - - + -
113U GLN 5.1 0.4 - - - -
118U ILE* 5.7 0.2 - - + -
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Residues in contact with GLU 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ARG* 3.0 43.7 + - - -
62U GLU* 4.9 8.8 - - + +
64U TYR 4.1 4.7 - - - +
65U ILE* 5.9 0.2 - - - -
82U LYS* 5.4 2.7 - - - -
83U PHE* 1.3 77.7 - - - +
85U VAL* 1.3 66.1 + - - +
86U GLU 3.9 0.4 - - - -
108U ILE* 3.3 6.9 - - - +
109U ARG* 2.9 46.2 + - + +
110U LYS* 3.9 36.5 + - - +
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Residues in contact with VAL 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62U LYS* 3.6 44.2 + - + +
64U TYR* 3.9 30.5 + - + +
66U VAL* 3.9 23.3 - - + -
84U GLU* 1.3 78.7 + - - +
86U GLU* 1.3 60.9 + - - +
87U ASN 3.3 29.4 - - - +
88U LEU* 4.1 7.4 - - + +
106U LEU* 3.9 18.2 - - + -
107U LYS 3.5 6.3 - - - +
108U ILE* 4.9 0.4 - - + -
109U ARG* 5.5 0.2 - - - -
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Residues in contact with GLU 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62U LYS* 2.8 26.9 + - - +
84U GLU 3.7 2.8 + - - -
85U VAL* 1.3 73.0 - - - +
87U ASN* 1.3 59.5 + - + +
107U LYS* 2.7 53.4 + - + +
108U ILE 4.5 0.9 - - - +
109U ARG* 3.4 56.3 - - + +
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Residues in contact with ASN 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U TRP* 4.9 2.9 - - + -
62U LYS* 4.3 6.9 - - - +
85U VAL* 3.3 8.5 - - - +
86U GLU* 1.3 84.3 + - + +
88U LEU* 1.3 74.2 + - - +
89U ILE* 3.6 26.8 - - + +
105U LEU 3.7 1.0 - - - +
106U LEU* 3.5 2.6 - - - -
107U LYS* 2.9 42.3 + - + -
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Residues in contact with LEU 88 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59U PHE* 4.0 40.4 - - + -
60U PRO* 4.0 31.9 - - + -
62U LYS* 4.0 23.5 - - + +
64U TYR* 4.3 14.6 - - + -
85U VAL* 4.1 3.6 - - + +
87U ASN* 1.3 81.7 + - - +
89U ILE* 1.3 63.5 + - - +
90U LEU* 3.8 16.6 + - + +
104U ALA* 5.3 0.2 - - + -
105U LEU 3.8 0.7 - - - +
106U LEU* 3.8 28.9 - - + -
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Residues in contact with ILE 89 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U TRP* 3.9 16.8 - - + -
87U ASN* 3.6 28.0 - - - +
88U LEU* 1.3 70.3 - - - +
90U LEU* 1.3 67.6 - - - +
104U ALA* 3.3 8.1 - - - +
105U LEU* 2.8 45.6 + - + +
237U TRP* 3.9 18.9 - - + -
241U HIS* 3.7 56.3 - - + +
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Residues in contact with LEU 90 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56U THR* 3.7 16.8 - - + +
59U PHE* 3.9 37.9 - - + +
60U ILE* 4.2 53.8 - - + +
88U LEU* 3.8 15.7 + - + +
89U ILE* 1.3 86.0 - - - +
91U HIS* 1.3 65.9 + - - +
92U LYS* 3.4 3.1 + - - +
104U ALA* 4.0 8.1 - - + -
237U TRP* 4.2 3.4 + - - -
241U HIS* 5.9 0.9 - - - -
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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