Contacts of the strand formed by residues 102 - 106 (chain E) in PDB entry 5JLH
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 VAL 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E LEU* 3.5 20.0 - - + +
9E ILE* 4.3 20.0 - - + -
89E PHE* 4.4 10.3 - - + -
97E PRO* 6.2 3.4 - - + -
100E HIS 4.8 2.0 - - - +
101E PRO* 1.3 75.3 - - - +
103E LEU* 1.3 73.2 + - - +
104E LEU* 4.0 2.4 + - + -
122E MET* 3.8 30.1 - - + -
128E THR* 4.2 10.3 - - + +
130E ALA 3.0 7.9 + - - +
131E MET* 3.0 35.8 - - + +
132E TYR 3.1 3.8 + - - +
355E TRP* 3.8 4.0 - - - -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU 2.8 14.8 + - - +
8E VAL* 3.8 10.5 - - + -
9E ILE* 2.8 27.4 + - - -
102E VAL* 1.3 75.7 - - - +
104E LEU* 1.3 81.9 + - - +
132E TYR* 3.6 33.7 - - + +
134E ALA* 3.8 8.3 - - + -
139E LEU* 4.2 9.0 - - + -
342E GLY* 3.3 42.4 - - - +
345E LEU* 4.6 10.5 - - + -
346E ALA* 4.9 2.9 - - + +
351E PHE* 4.9 4.3 - - + -
355E TRP* 4.1 12.8 - - + -
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 3.4 29.6 - - + +
11E ASN* 5.6 3.1 - - + +
85E TRP* 3.9 24.0 - - + +
102E VAL* 4.9 2.7 - - + +
103E LEU* 1.3 83.3 - - - +
105E THR* 1.3 67.0 + - - +
118E MET* 3.3 37.2 - - + -
122E MET* 3.8 35.7 - - + -
131E MET* 3.9 10.1 - - + -
132E TYR 2.8 12.1 + - - +
133E VAL* 3.3 5.4 - - + -
134E ALA* 2.8 25.1 + - - -
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Residues in contact with THR 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE 3.1 8.8 + - - -
10E ASP* 3.2 42.2 - - - +
11E ASN* 3.5 12.6 + - - +
103E LEU* 5.0 0.2 - - - +
104E LEU* 1.3 82.8 - - - +
106E GLU* 1.3 66.4 + - - +
118E MET* 4.2 7.3 - - - +
134E ALA 3.4 6.7 + - - -
136E GLN* 2.9 40.5 - - + +
139E LEU* 4.2 9.9 - - - +
338E VAL* 3.4 16.4 - - - +
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASN 5.6 1.3 - - - -
73E GLY 5.4 0.9 - - - +
105E THR* 1.3 82.0 + - - +
107E ALA* 1.3 88.9 + - - +
110E ASN* 3.4 30.1 - - - +
111E PRO 4.1 4.0 - - - +
114E ASN* 4.3 2.6 - - + +
115E ARG* 3.1 52.1 + - + +
118E MET* 4.6 20.4 - - + -
133E VAL* 5.1 3.1 - - + -
134E ALA 2.8 15.6 + - - +
135E ILE* 3.4 3.5 - - - +
136E GLN* 2.9 31.4 + - - +
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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