Contacts of the strand formed by residues 130 - 140 (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 ILE 130 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110H LEU* 4.4 17.9 - - + -
111H VAL 3.7 5.2 - - - +
112H LEU* 4.7 4.0 - - + +
113H ASN* 3.2 8.6 + - - +
126H LEU* 3.5 19.1 - - + +
127H TYR* 3.3 20.6 + - + +
128H ASN 4.9 0.9 - - - +
129H ALA* 1.3 74.0 - - - +
131H GLU* 1.3 60.3 + - - +
132H TRP 3.6 24.7 - - - +
133H VAL* 4.1 5.8 - - + -
173H PRO* 3.4 34.7 - - + +
178H LEU* 5.2 2.9 - - + -
205H LEU* 3.5 40.6 - - + -
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Residues in contact with GLU 131 (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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111H VAL* 2.7 27.9 + - - +
112H LEU 3.9 11.9 - - - +
113H ASN* 3.2 24.9 + - - +
129H ALA 3.5 0.6 + - - -
130H ILE* 1.3 74.6 - - - +
132H TRP* 1.3 70.7 + - + +
172H ARG* 3.2 40.4 + - - +
173H PRO* 3.8 6.3 - - - +
225H GLY* 5.3 2.4 - - - -
128J ASN* 2.8 35.8 + - - +
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Residues in contact with TRP 132 (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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109H ALA 3.9 0.2 - - - +
110H LEU* 3.4 4.2 - - - -
111H VAL* 2.9 42.9 + - + -
130H ILE* 3.6 5.6 - - - +
131H GLU* 1.3 99.7 - - + +
133H VAL* 1.3 64.2 + - - +
134H LEU* 4.2 15.2 - - + +
170H ALA* 3.7 29.6 - - + -
171H GLN 3.4 20.0 - - - -
172H ARG* 3.3 44.4 - - + -
124J ASP 5.2 4.3 - - - -
127J TYR* 4.4 15.3 - + + -
128J ASN* 2.8 40.0 - - + +
173J PRO* 4.9 9.9 - - + -
174J ALA* 3.8 29.2 - - + -
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Residues in contact with VAL 133 (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* 4.2 10.1 - - + -
109H ALA 3.3 3.1 - - - -
110H LEU* 3.8 15.0 - - + -
130H ILE* 4.1 9.4 - - + -
132H TRP* 1.3 75.7 - - - +
134H LEU* 1.3 64.1 + - - +
171H GLN* 2.8 38.5 + - - +
173H PRO* 4.0 18.2 - - + -
176H LEU* 3.6 34.1 - - + -
178H LEU* 4.0 21.8 - - + -
252H ILE* 4.3 11.7 - - + -
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Residues in contact with LEU 134 (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* 3.8 2.1 - - - +
109H ALA* 2.8 58.2 + - + +
111H VAL* 4.0 25.8 - - + -
132H TRP* 4.2 8.7 - - + -
133H VAL* 1.3 78.5 - - - +
135H PRO* 1.3 76.0 - - + +
166H ILE* 4.0 20.4 - - + -
167H GLY 4.4 2.7 - - - +
169H PRO 4.3 4.0 - - - +
170H ALA* 3.8 15.0 - - + -
227H ILE* 5.1 0.9 - - + -
252H ILE* 4.2 5.2 - - - -
124J ASP* 4.8 8.7 - - + -
127J TYR* 3.7 35.0 - - + -
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Residues in contact with PRO 135 (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 3.9 4.9 - - - +
108H ILE* 5.0 0.4 - - - -
134H LEU* 1.3 91.9 - - + +
136H ALA* 1.3 59.6 + - - +
166H ILE* 3.8 2.3 - - - +
167H GLY* 2.9 26.9 + - - -
168H GLY 3.6 17.7 - - - +
169H PRO 3.9 12.6 - - - +
249H ILE* 3.8 17.7 - - + -
252H ILE* 3.8 17.7 - - + +
253H GLY 3.9 2.2 - - - -
254H SER 3.6 29.4 - - - +
255H VAL* 3.8 13.2 - - + -
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Residues in contact with ALA 136 (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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106H ALA* 3.6 4.7 - - - +
107H GLU* 2.8 38.1 + - + +
109H ALA* 4.1 11.2 - - + -
135H PRO* 1.3 76.4 - - - +
137H LEU* 1.3 63.7 + - - +
164H TYR* 5.6 0.4 - - + -
165H VAL 3.2 12.3 - - - +
166H ILE* 4.5 5.4 - - + -
229H LEU* 3.9 27.8 - - + -
249H ILE* 4.8 0.5 - - - +
255H VAL* 3.7 12.2 - - - +
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Residues in contact with LEU 137 (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* 4.2 13.7 - - + -
105H GLU 3.4 8.3 - - - +
106H ALA* 4.3 1.1 - - - -
107H GLU* 5.3 0.2 - - - -
136H ALA* 1.3 79.6 - - - +
138H GLU* 1.3 59.9 + - - +
139H VAL 4.1 0.4 - - - -
164H TYR* 3.3 6.2 - - - +
165H VAL* 2.9 43.0 + - + +
185H MET* 3.9 20.0 - - + -
229H LEU* 5.7 0.2 - - - -
245H PHE* 4.5 11.2 - - + +
246H GLU 5.2 0.2 - - - -
247H ALA* 3.8 28.9 - - + +
255H VAL* 3.8 18.6 - - + +
256H ALA* 4.0 6.1 - - - -
257H ALA* 3.9 37.0 - - + +
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Residues in contact with GLU 138 (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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60H LYS* 3.1 49.2 + - - +
82H LEU* 5.0 1.2 - - + +
86H MET* 5.7 0.9 - - + +
104H ILE* 3.2 3.6 - - - -
105H GLU* 2.8 41.4 + - + +
107H GLU* 3.1 33.9 - - - +
136H ALA 4.2 0.6 - - - -
137H LEU* 1.3 72.2 - - - +
139H VAL* 1.3 62.7 + - - +
140H VAL* 3.4 15.9 + - - +
161H CYS* 3.7 15.9 - - - -
162H GLY 4.6 1.2 + - - -
163H VAL 3.8 10.5 - - - +
164H TYR* 4.2 1.3 - - + -
229H LEU* 3.8 18.6 - - + -
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Residues in contact with VAL 139 (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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94H ILE* 4.3 7.6 - - + -
99H VAL* 4.1 13.9 - - + -
102H PRO* 4.0 23.6 - - + -
103H ARG 3.2 11.7 - - - +
104H ILE* 3.5 18.6 - - + -
138H GLU* 1.3 70.2 - - - +
140H VAL* 1.3 59.7 + - - +
162H GLY* 3.2 8.0 + - - -
163H VAL* 2.9 52.1 + - + +
165H VAL* 4.7 8.3 - - + -
239H VAL* 4.9 0.2 - - + -
259H PHE* 3.8 27.4 - - + -
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Residues in contact with VAL 140 (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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60H LYS* 4.0 3.6 - - - +
99H VAL* 3.6 2.6 - - - +
101H GLN 4.0 0.3 - - - +
102H PRO* 3.3 4.9 - - - +
103H ARG* 2.7 54.7 + - + +
105H GLU* 3.8 16.4 - - - +
138H GLU* 3.4 21.3 + - + +
139H VAL* 1.3 76.4 - - - +
141H GLY* 1.3 58.7 + - - +
147H TRP* 3.6 22.4 - - + -
160H SER* 3.2 16.6 - - - +
162H GLY 4.2 0.4 - - - +
236H MET* 3.9 13.9 - - + -
1263H PO4 3.4 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