Contacts of the strand formed by residues 103 - 112 (chain H) in PDB entry 2WQT
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 ARG 103 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101H GLN 4.0 0.7 - - - -
102H PRO* 1.3 78.3 - - - +
104H ILE* 1.3 58.2 + - - +
139H VAL* 3.2 3.6 - - - -
140H VAL* 2.7 51.4 + - + +
147H TRP* 3.3 64.8 - - - +
236H MET* 3.8 32.7 - - + +
237H VAL 3.2 19.1 - - - +
238H ALA* 3.7 16.1 - - - +
239H VAL* 3.9 4.3 - - - -
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Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H ARG* 1.3 72.6 - - - +
105H GLU* 1.3 61.3 + - - +
137H LEU* 4.2 22.0 - - + -
138H GLU 3.2 9.4 - - - +
139H VAL* 3.5 31.0 - - + -
185H MET* 3.9 13.5 - - + +
236H MET* 3.3 5.0 - - - -
237H VAL* 3.0 41.4 + - + +
239H VAL* 3.4 15.0 - - + -
245H PHE* 3.1 48.5 - - + -
257H ALA* 6.0 0.2 - - + -
259H PHE* 4.7 5.8 - - + -
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Residues in contact with GLU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ILE* 1.3 75.6 - - - +
106H ALA* 1.3 60.1 + - - +
107H GLU* 3.0 22.5 - - + +
137H LEU* 3.4 7.8 - - - +
138H GLU* 2.8 43.2 + - + +
140H VAL* 3.8 8.4 - - - +
185H MET* 4.5 6.3 - - - -
232H ALA* 3.5 25.1 - - + +
234H GLY 4.2 6.1 - - - +
235H PRO 5.2 0.2 - - - -
236H MET* 3.7 24.7 + - + +
1263H PO4 2.7 38.6 + - - -
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Residues in contact with ALA 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H GLU* 1.3 73.5 - - - +
107H GLU* 1.3 62.9 + - - +
136H ALA 3.6 6.3 - - - +
137H LEU* 4.3 2.9 - - + -
183H MET* 3.8 39.3 - - + +
185H MET* 4.4 6.6 - - - +
232H ALA* 3.6 0.7 - - - -
233H LEU* 2.9 31.4 + - + +
234H GLY 5.1 1.0 + - - -
247H ALA* 3.8 22.7 - - + -
249H ILE* 4.7 2.9 - - + -
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Residues in contact with GLU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H VAL 4.5 2.0 - - - +
105H GLU* 3.0 34.5 - - + +
106H ALA* 1.3 78.5 - - - +
108H ILE* 1.3 66.6 + - - +
136H ALA* 2.8 40.8 + - + +
138H GLU* 3.1 24.3 - - + +
229H LEU* 3.3 21.9 - - + +
230H THR 4.9 0.2 - - - +
231H GLY* 3.0 38.8 + - - +
232H ALA* 3.5 8.2 + - - +
233H LEU* 4.1 6.3 - - - +
249H ILE* 3.6 7.4 - - - +
1263H PO4 4.1 1.9 + - - -
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Residues in contact with ILE 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H GLU* 1.3 77.1 - - - +
109H ALA* 1.3 68.7 + - - +
110H LEU* 4.1 16.4 - - + -
133H VAL* 4.2 13.5 - - + -
134H LEU 3.9 2.9 - - - +
178H LEU* 4.2 8.7 - - + -
181H CYS* 3.5 32.3 - - - -
204H PRO* 3.8 22.9 - - + -
229H LEU* 4.0 0.6 - - - -
230H THR* 2.7 48.8 + - - +
231H GLY 4.4 1.2 + - - -
233H LEU* 4.2 16.1 - - + +
249H ILE* 4.5 6.1 - - + -
252H ILE* 3.7 20.0 - - + -
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Residues in contact with ALA 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H GLU 4.0 1.0 + - - -
108H ILE* 1.3 73.9 - - - +
110H LEU* 1.3 64.2 + - - +
133H VAL* 3.3 5.9 - - - +
134H LEU* 2.8 51.3 + - + +
136H ALA* 4.1 7.9 - - + -
166H ILE* 4.9 2.2 - - + -
227H ILE* 4.1 17.9 - - + -
228H ILE 3.3 5.8 - - - +
229H LEU* 3.7 23.6 - - + -
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H ILE* 4.1 11.4 - - + -
109H ALA* 1.3 83.3 - - - +
111H VAL* 1.3 65.9 + - - +
112H LEU* 5.1 3.8 - - + -
126H LEU* 4.7 1.1 - - + -
130H ILE* 4.4 18.4 - - + -
132H TRP 3.4 3.8 - - - +
133H VAL* 3.8 20.9 - - + -
178H LEU* 5.3 2.7 - - + -
204H PRO* 6.1 0.4 - - + -
205H LEU* 3.7 32.3 - - + -
208H ALA* 3.7 16.6 - - + -
226H ASP 3.7 0.9 - - - +
227H ILE* 3.3 6.1 - - - +
228H ILE* 2.8 49.1 + - + +
230H THR* 3.7 24.7 - - + -
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Residues in contact with VAL 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LEU* 1.3 78.3 - - - +
112H LEU* 1.3 60.6 + - - +
130H ILE* 3.6 4.3 - - - -
131H GLU* 2.7 48.4 + - - +
132H TRP* 2.9 28.3 + - + +
134H LEU* 4.0 22.7 - - + -
225H GLY* 3.9 22.4 - - - +
226H ASP 3.4 3.4 - - - +
227H ILE* 4.4 8.5 - - + -
124J ASP* 4.4 24.0 - - + +
128J ASN* 6.0 1.8 - - + -
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Residues in contact with LEU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LEU* 5.1 7.2 - - + -
111H VAL* 1.3 79.5 - - - +
113H ASN* 1.4 59.7 + - - +
114H ARG 3.3 12.8 - - - +
116H LEU* 4.0 21.8 - - + -
126H LEU* 5.2 5.4 - - + -
129H ALA* 3.2 18.6 - - + +
130H ILE* 5.1 4.9 - - + -
131H GLU* 3.9 10.4 - - - +
222H LEU* 3.8 34.3 - - + -
223H ARG 3.9 15.0 - - - +
224H THR* 4.1 0.3 + - - -
225H GLY* 2.9 24.1 + - - -
226H ASP* 3.2 21.3 + - + +
228H ILE* 3.9 20.9 - - + -
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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