Contacts of the strand formed by residues 104 - 109 (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 ALA 104 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53U ILE* 3.4 7.9 - - - +
54U SER 2.7 35.7 + - - +
55U ALA 3.8 7.4 - - - +
56U THR* 3.7 21.5 - - - +
59U PHE* 4.1 11.4 - - + -
88U LEU* 5.3 0.2 - - + -
89U ILE 3.3 13.2 - - - +
90U LEU* 4.0 9.9 - - + -
103U ILE* 1.3 76.4 - - - +
105U LEU* 1.3 64.9 + - - +
106U LEU* 4.5 2.9 - - + -
237U TRP* 4.1 2.7 - - - -
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Residues in contact with LEU 105 (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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47U ILE* 4.1 26.0 - - + -
51U TRP* 4.0 14.8 - - + -
52U VAL 3.5 9.6 - - - +
53U ILE* 4.2 12.3 - - + -
87U ASN 3.7 1.6 - - - +
88U LEU* 3.8 1.7 - - - +
89U ILE* 2.8 44.5 + - + +
104U ALA* 1.3 76.9 - - - +
106U LEU* 1.3 63.6 + - - +
107U LYS 4.2 0.2 - - - -
237U TRP* 3.5 29.2 - - + -
238U ILE* 4.2 9.2 - - + +
241U HIS* 3.8 27.1 - - + -
242U THR* 3.8 20.6 - - + -
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Residues in contact with LEU 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U ILE* 3.9 24.0 - - + -
51U TRP* 3.6 4.5 - - - -
52U VAL* 2.8 47.6 + - + +
54U SER* 4.1 14.6 - - - -
59U PHE* 3.9 35.2 - - + -
64U TYR* 5.3 1.6 - - + -
66U VAL* 4.0 7.9 - - + -
85U VAL* 3.9 28.9 - - + -
87U ASN 3.5 3.8 - - - -
88U LEU* 3.8 15.0 - - + -
104U ALA 4.4 0.7 - - - +
105U LEU* 1.3 82.4 - - - +
107U LYS* 1.3 60.9 + - - +
108U ILE* 3.5 6.7 + - + +
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Residues in contact with LYS 107 (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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50U CYS* 3.3 30.1 - - - +
51U TRP* 3.6 40.0 - - + +
85U VAL* 3.5 4.9 - - - -
86U GLU* 2.7 64.8 + - + +
87U ASN* 2.9 25.3 + - + +
106U LEU* 1.3 71.9 - - - +
108U ILE* 1.3 60.2 + - - +
111U CYS* 5.5 1.1 - - - -
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Residues in contact with ILE 108 (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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46U LEU* 4.0 20.9 - - + -
49U PRO 4.0 16.2 - - - +
50U CYS 3.0 18.4 + - - +
52U VAL* 4.2 9.6 - - + -
66U VAL* 4.0 32.3 - - + -
68U LEU* 4.0 17.0 - - + -
83U PHE* 3.8 21.1 - - + -
84U GLU 3.3 11.4 - - - +
85U VAL* 4.9 0.4 - - + -
86U GLU* 4.5 1.9 - - - +
106U LEU* 4.1 11.0 - - + +
107U LYS* 1.3 81.4 - - - +
109U ARG* 1.3 66.9 + - - +
111U CYS* 3.9 17.3 - - - -
112U ALA* 4.6 0.7 - - + +
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Residues in contact with ARG 109 (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 GLU* 5.7 5.3 - - - +
83U PHE* 3.6 5.4 - - - -
84U GLU* 2.9 38.4 + - + +
85U VAL 5.5 0.2 - - - -
86U GLU* 3.4 47.3 + - + +
108U ILE* 1.3 79.1 - - - +
110U SER* 1.3 100.6 - - + +
111U CYS* 5.6 1.1 - - - -
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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