Contacts of the strand formed by residues 103 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLN 4.0 0.7 - - - -
102A PRO* 1.3 77.8 - - - +
104A ILE* 1.3 58.1 + - - +
139A VAL* 3.3 3.3 - - - -
140A VAL* 2.7 51.6 + - + +
147A TRP* 3.2 64.8 - - - +
236A MET* 3.8 34.1 - - + +
237A VAL 3.2 18.2 - - - +
238A ALA* 3.7 16.8 - - + +
239A VAL* 4.0 4.3 - - - -
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Residues in contact with ILE 104 (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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103A ARG* 1.3 71.1 - - - +
105A GLU* 1.3 61.8 + - - +
137A LEU* 4.2 20.6 - - + -
138A GLU 3.2 9.6 - - - +
139A VAL* 3.5 31.6 - - + -
185A MET* 3.9 12.8 - - + +
236A MET* 3.3 4.1 - - - -
237A VAL* 3.0 44.6 + - + +
239A VAL* 3.5 15.0 - - + -
245A PHE* 3.1 49.1 - - + -
257A ALA* 6.1 0.7 - - + -
259A PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (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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104A ILE* 1.3 76.2 - - - +
106A ALA* 1.3 60.6 + - - +
107A GLU* 3.0 18.7 - - - +
137A LEU* 3.4 9.0 - - - +
138A GLU* 2.8 42.4 + - + +
140A VAL* 3.7 12.1 - - - +
185A MET* 4.5 6.1 - - - -
232A ALA* 3.4 26.6 - - + +
234A GLY 4.2 7.0 - - - +
235A PRO 5.2 0.2 - - - -
236A MET* 3.8 22.6 + - + +
1264A PO4 2.8 40.2 + - - -
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Residues in contact with ALA 106 (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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105A GLU* 1.3 73.6 - - - +
107A GLU* 1.3 61.6 + - - +
136A ALA 3.5 6.7 - - - +
137A LEU* 4.2 2.2 - - + -
183A MET* 3.8 37.1 - - + +
185A MET* 4.5 6.2 - - - +
232A ALA* 3.7 0.5 - - - -
233A LEU* 2.9 32.7 + - + +
234A GLY 5.2 0.8 + - - -
247A ALA* 3.8 24.0 - - + -
249A ILE* 4.7 2.9 - - + -
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Residues in contact with GLU 107 (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 4.5 1.4 - - - +
105A GLU* 3.0 34.2 - - + +
106A ALA* 1.3 79.0 - - - +
108A ILE* 1.3 66.2 + - - +
136A ALA* 2.8 41.8 + - + +
138A GLU* 3.1 24.1 - - + +
229A LEU* 3.3 22.1 - - + +
231A GLY* 2.9 38.4 + - - +
232A ALA* 3.5 7.9 + - - +
233A LEU* 4.1 6.8 - - - +
249A ILE* 3.7 7.3 - - - +
1264A PO4 4.2 1.9 + - - -
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Residues in contact with ILE 108 (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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107A GLU* 1.3 76.2 - - - +
109A ALA* 1.3 68.6 + - - +
110A LEU* 4.1 15.9 - - + -
133A VAL* 4.1 13.7 - - + -
134A LEU 3.8 3.8 - - - +
178A LEU* 4.2 8.5 - - + -
181A CYS* 3.5 31.6 - - - -
204A PRO* 3.9 23.1 - - + -
229A LEU* 4.0 1.0 - - - -
230A THR* 2.7 46.5 + - - +
231A GLY 4.4 1.4 + - - -
233A LEU* 4.2 18.4 - - + +
249A ILE* 4.6 5.2 - - + -
252A ILE* 3.8 18.4 - - + -
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Residues in contact with ALA 109 (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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107A GLU 4.0 1.0 + - - -
108A ILE* 1.3 74.7 - - - +
110A LEU* 1.3 64.3 + - - +
133A VAL* 3.4 5.4 - - - +
134A LEU* 2.8 47.7 + - + +
136A ALA* 4.1 8.5 - - + -
166A ILE* 5.0 2.0 - - + -
227A ILE* 4.2 18.4 - - + -
228A ILE 3.3 6.1 - - - +
229A LEU* 3.7 22.9 - - + -
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Residues in contact with LEU 110 (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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108A ILE* 4.1 11.7 - - + -
109A ALA* 1.3 83.1 - - - +
111A VAL* 1.3 65.5 + - - +
112A LEU* 5.1 4.3 - - + -
126A LEU* 4.7 1.1 - - + -
130A ILE* 4.4 20.9 - - + -
132A TRP 3.5 3.1 - - - +
133A VAL* 3.8 21.1 - - + -
178A LEU* 5.2 3.6 - - + -
204A PRO* 6.1 0.2 - - + -
205A LEU* 3.7 30.7 - - + -
208A ALA* 3.8 24.2 - - + -
226A ASP 3.7 0.5 - - - +
227A ILE* 3.3 6.8 - - - +
228A ILE* 2.8 45.1 + - + +
230A THR* 3.8 15.9 - - + -
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Residues in contact with VAL 111 (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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110A LEU* 1.3 77.7 - - - +
112A LEU* 1.3 59.6 + - - +
130A ILE* 3.6 4.3 - - - +
131A GLU* 2.7 48.0 + - - +
132A TRP* 2.9 28.0 + - + +
134A LEU* 3.9 22.9 - - + -
225A GLY* 3.9 22.7 - - - +
226A ASP 3.4 2.7 - - - -
227A ILE* 4.4 14.8 - - + -
124D ASP* 4.6 15.7 - - + +
128D ASN* 5.9 2.0 - - + +
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Residues in contact with LEU 112 (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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110A LEU* 5.1 8.1 - - + -
111A VAL* 1.3 78.4 - - - +
113A ASN* 1.3 59.2 + - - +
114A ARG 3.9 13.2 - - - +
116A LEU* 4.0 22.0 - - + -
126A LEU* 5.2 5.4 - - + -
129A ALA* 3.1 18.6 - - + +
130A ILE* 5.1 3.8 - - + -
131A GLU* 3.9 11.0 - - - +
222A LEU* 3.8 33.9 - - + -
223A ARG 3.9 16.4 - - - +
224A THR* 4.0 0.3 + - - -
225A GLY* 2.9 24.8 + - - +
226A ASP* 3.2 21.7 + - + +
228A ILE* 3.9 21.1 - - + -
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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