Contacts of the strand formed by residues 153 - 165 (chain A) in PDB entry 5V8V
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 THR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A THR* 3.8 15.2 - - + +
147A LEU 3.2 9.4 + - - -
148A ARG* 4.2 9.4 + - - +
149A TYR* 5.3 1.7 - - - -
151A THR* 5.3 0.6 - - - +
152A GLY* 1.3 79.4 + - - -
154A VAL* 1.3 76.1 + - - +
155A SER* 3.6 14.6 - - - +
179A GLU* 4.1 3.1 - - + +
181A PRO* 3.4 29.0 - - - +
185A PHE* 5.2 2.3 - - - -
317B ARG* 5.3 3.1 + - - -
360B LYS* 6.3 0.9 - - - +
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Residues in contact with VAL 154 (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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111A TRP* 4.2 19.1 - - + +
147A LEU* 2.9 57.7 + - + -
149A TYR* 4.5 4.8 - - + -
153A THR* 1.3 74.3 - - - +
155A SER* 1.3 67.3 + - - +
177A VAL* 4.0 25.4 - - + -
179A GLU 3.4 13.2 - - - +
180A MET* 4.5 1.8 - - + -
181A PRO* 4.5 0.4 - - + -
185A PHE* 3.4 39.3 - - + -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 3.3 6.3 - - - -
146A THR* 3.0 21.8 + - - +
153A THR* 3.6 12.3 - - - +
154A VAL* 1.3 77.9 + - - +
156A GLY* 1.3 52.9 + - - +
177A VAL* 3.3 8.9 - - - -
178A THR* 2.7 31.5 + - - -
179A GLU* 3.2 38.4 + - - -
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Residues in contact with GLY 156 (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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144A GLU* 3.4 6.8 - - - +
145A LEU* 2.6 40.4 + - - +
155A SER* 1.3 78.2 - - - +
157A PHE* 1.3 58.1 + - - -
175A GLY* 6.0 0.2 - - - -
176A GLU 3.3 12.1 - - - -
177A VAL* 4.2 0.9 - - - -
178A THR* 3.6 13.5 - - - -
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Residues in contact with PHE 157 (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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114A SER* 3.8 0.9 - - - -
116A LYS* 3.4 37.0 - - + -
138A TYR* 4.7 6.3 - - - -
140A HIS* 5.6 3.6 - + - -
142A GLY* 3.6 28.9 - - - +
143A THR 3.2 6.3 - - - +
144A GLU* 4.6 1.3 - - - -
145A LEU* 4.2 2.9 - - - +
156A GLY* 1.3 76.1 - - - -
158A LEU* 1.3 71.0 + - - +
159A SER* 3.3 18.2 - - - -
175A GLY* 3.5 3.0 - - - -
176A GLU* 2.7 59.5 + - + -
178A THR* 3.9 22.2 - - + -
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Residues in contact with LEU 158 (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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109A ASN* 5.5 0.9 - - - +
141A ASN* 3.7 15.1 + - - +
142A GLY 2.9 25.0 + - - -
143A THR* 2.7 38.0 + - + +
144A GLU 5.2 0.7 - - - +
145A LEU* 4.1 30.7 - - + -
157A PHE* 1.3 76.6 - - - +
159A SER* 1.3 64.2 + - - +
173A MET* 4.0 18.8 - - + -
174A PHE* 3.5 14.8 - - - +
204A GLY* 5.8 3.4 - - - +
206A VAL* 3.9 32.3 - - + -
501A NAG 5.3 7.4 - - - +
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Residues in contact with SER 159 (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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138A TYR* 3.5 17.0 + - - -
139A LYS 4.4 3.8 - - - -
141A ASN 4.5 2.5 - - - +
157A PHE* 3.3 11.6 - - - -
158A LEU* 1.3 76.0 + - - +
160A GLN* 1.3 61.2 + - - +
173A MET* 3.3 8.8 - - - +
174A PHE* 2.8 43.7 + - - +
176A GLU* 2.6 38.7 + - - -
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Residues in contact with GLN 160 (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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138A TYR* 3.5 3.1 - - - -
139A LYS* 2.8 72.5 + - + +
141A ASN* 5.8 0.4 - - + -
159A SER* 1.3 77.2 - - - +
161A ASP* 1.3 67.7 + - - +
171A THR* 3.4 28.2 - - + +
172A GLN 3.3 15.7 - - - +
173A MET* 4.0 23.9 - - + +
174A PHE* 4.0 1.3 - - - -
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Residues in contact with ASP 161 (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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92A ILE* 4.0 8.3 - - + -
93A GLY* 3.3 11.7 - - - -
130A PHE* 3.5 7.4 - - + -
135A SER* 2.5 31.0 + - - -
137A SER* 2.6 28.7 + - - -
138A TYR* 3.3 15.7 - - + +
160A GLN* 1.3 75.7 - - - +
162A ILE* 1.3 78.8 + - - +
163A ILE* 3.5 4.1 + - - +
171A THR* 4.4 4.3 - - - -
172A GLN* 3.0 30.8 + - - +
174A PHE* 3.8 16.6 - - + -
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Residues in contact with ILE 162 (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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91A GLY 3.7 0.5 - - - +
92A ILE* 3.3 3.8 - - - -
93A GLY* 2.8 32.8 + - - +
94A THR* 5.0 3.1 - - - +
137A SER* 3.8 24.7 - - - +
161A ASP* 1.3 82.7 + - - +
163A ILE* 1.3 63.2 + - - +
164A THR* 4.2 7.6 - - + +
169A THR* 4.3 21.5 - - + -
170A VAL 3.4 11.7 - - - +
171A THR* 4.0 16.4 - - - +
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Residues in contact with ILE 163 (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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90A ILE* 4.3 17.9 - - + -
91A GLY 3.2 6.7 - - - +
92A ILE* 4.0 22.7 - - + -
110A VAL* 4.3 19.7 - - + -
161A ASP 4.0 3.8 - - - +
162A ILE* 1.3 78.5 - - - +
164A THR* 1.3 70.7 + - - +
165A VAL 4.1 0.6 + - - +
168A ILE 3.9 0.3 - - - +
169A THR* 3.4 0.7 - - - -
170A VAL* 2.7 42.9 + - + +
172A GLN* 3.6 35.0 - - + -
174A PHE* 4.3 13.0 - - + -
209A ILE* 4.0 18.2 - - + -
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Residues in contact with THR 164 (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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90A ILE* 3.3 9.7 - - - +
91A GLY* 2.7 45.4 + - - +
93A GLY 5.8 2.0 - - - +
96A PRO* 5.0 13.7 - - + +
162A ILE* 4.7 8.5 - - + +
163A ILE* 1.3 76.1 - - - +
165A VAL* 1.3 60.4 + - - +
166A GLY 4.3 6.3 - - - -
168A ILE 3.3 5.2 - - - -
169A THR* 3.5 27.1 - - + +
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Residues in contact with VAL 165 (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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74A SER* 4.2 0.2 + - - -
76A VAL* 3.7 19.3 - - + -
89A GLU 4.8 2.2 - - - +
90A ILE* 3.9 13.2 - - + -
103A PHE* 4.1 25.4 - - + -
163A ILE* 5.1 2.2 - - + +
164A THR* 1.3 74.8 - - - +
166A GLY* 1.3 67.4 + - - +
167A GLY 3.4 0.2 + - - -
168A ILE* 2.8 28.6 + - + +
170A VAL* 5.2 1.3 - - + -
209A ILE* 4.5 16.6 - - + -
213A ILE* 4.1 26.0 - - + -
244A LEU* 4.0 17.4 - - + +
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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