Contacts of the strand formed by residues 140 - 149 (chain H) in PDB entry 2CK0
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 140 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H PRO* 5.2 8.3 - - + -
139H MET* 1.3 78.2 - - - +
141H THR* 1.3 64.9 + - - +
142H LEU* 3.8 10.4 + - + +
186H THR* 4.3 2.9 - - - +
187H VAL* 2.8 40.7 + - + +
188H PRO 4.5 2.2 - - - +
189H SER* 4.2 23.1 - - - +
192H ARG* 4.6 22.0 - - + +
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Residues in contact with THR 141 (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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130H PRO* 3.6 10.2 - - - +
139H MET 4.3 0.4 + - - -
140H VAL* 1.3 72.6 - - - +
142H LEU* 1.3 80.2 + - - +
184H SER* 4.2 16.6 - - - +
185H VAL 3.4 9.6 - - - +
186H THR* 3.6 19.6 + - - +
113L THR* 5.4 6.4 - - - +
115L SER* 4.0 21.5 + - - +
117L PHE* 3.4 21.5 - - + -
134L PHE* 4.3 7.0 - - + -
136L ASN* 5.1 5.2 - - - +
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Residues in contact with LEU 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU 3.8 4.7 - - - -
130H PRO* 3.8 14.8 - - + -
140H VAL* 4.1 15.7 - - + +
141H THR* 1.3 87.2 - - - +
143H GLY* 1.3 59.6 + - - +
184H SER* 3.4 2.3 - - - -
185H VAL* 2.8 41.7 + - + +
187H VAL* 4.4 3.6 - - + -
192H ARG* 3.8 45.8 - - + +
197H VAL* 3.6 36.8 - - + -
214H ILE* 4.1 19.7 - - + -
117L PHE* 4.0 5.4 - - - -
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Residues in contact with GLY 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU* 3.0 35.6 + - - +
142H LEU* 1.3 74.5 - - - +
144H CYS* 1.3 63.8 + - - +
158H TRP* 3.7 3.4 - - - -
183H SER 3.2 10.8 - - - -
214H ILE* 3.5 12.6 - - - +
117L PHE* 4.0 1.8 - - - -
134L PHE* 3.7 17.5 - - - -
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Residues in contact with CYS 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H VAL* 3.4 24.5 - - - -
126H TYR 3.7 7.6 - - - -
128H LEU* 4.0 5.1 - - - +
143H GLY* 1.3 76.7 - - - +
145H LEU* 1.3 61.0 + - - +
146H VAL* 3.8 5.1 + - + +
158H TRP* 3.7 12.1 - - + -
182H SER* 3.4 6.8 - - - -
183H SER* 2.8 32.2 + - - +
199H CYS* 2.0 50.0 - - - -
201H VAL* 4.6 0.9 - - - -
212H LYS* 4.7 2.7 - - - -
214H ILE* 4.8 2.9 - - - -
134L PHE* 4.7 0.2 - - - -
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Residues in contact with LEU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H SER 3.0 6.2 - - - +
125H VAL* 3.3 2.1 - - - -
126H TYR* 2.8 61.1 + - + +
128H LEU* 3.8 17.6 - - + +
144H CYS* 1.3 71.8 - - - +
146H VAL* 1.3 60.8 + - - +
147H LYS* 4.1 13.9 - - + -
180H THR* 4.2 19.5 - - + -
181H LEU 3.9 10.8 - - - +
182H SER* 4.6 9.9 - - - -
123L GLN* 4.4 3.4 - - - +
130L SER* 3.9 28.3 - - - +
132L VAL* 4.2 20.9 - - + -
177L THR* 4.6 6.7 - - + +
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Residues in contact with VAL 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 3.8 25.4 - - + -
124H SER 3.6 3.8 - - - -
125H VAL* 4.6 4.5 - - + +
144H CYS* 4.5 10.1 - - + +
145H LEU* 1.3 74.0 - - - +
147H LYS* 1.3 55.1 + - - +
149H TYR* 3.9 9.2 - - + -
154H VAL* 4.0 13.5 - - + -
156H VAL* 4.0 6.3 - - + -
180H THR* 3.6 0.7 - - - -
181H LEU* 2.7 63.6 + - + +
182H SER 5.7 0.2 - - - -
183H SER 5.7 0.2 - - - +
201H VAL* 3.9 38.1 - - + -
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Residues in contact with LYS 147 (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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124H SER* 3.0 39.8 + - - -
126H TYR* 3.8 31.6 - - + +
145H LEU* 4.1 9.8 - - + +
146H VAL* 1.3 75.2 - - - +
148H GLY* 1.3 66.0 + - - +
149H TYR* 3.6 2.7 - - - -
179H TYR 3.6 3.6 - - - -
180H THR* 3.4 33.5 + - + +
123L GLN* 4.0 18.6 - - - +
130L SER* 4.2 5.7 + - - -
177L THR* 5.6 1.8 - - - +
179L THR* 4.4 15.6 + - - +
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Residues in contact with GLY 148 (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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121H THR* 3.3 22.9 - - - +
122H PRO 3.3 6.5 - - - +
124H SER* 5.5 0.9 + - - -
147H LYS* 1.3 82.9 - - - +
149H TYR* 1.3 57.6 + - - -
178H LEU* 3.5 20.8 - - - +
179H TYR 2.7 14.6 + - - -
180H THR* 3.9 2.2 + - - -
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Residues in contact with TYR 149 (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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121H THR 3.2 11.7 - - - +
122H PRO 4.0 0.2 - - - -
123H PRO* 3.3 35.0 - - + -
146H VAL* 3.9 24.0 - - + -
148H GLY* 1.3 79.6 - - - +
150H PHE* 1.3 68.4 + - - +
151H PRO 3.7 15.5 - - - -
152H GLU* 3.1 25.7 + - - -
154H VAL* 3.4 27.3 - - + +
172H ALA* 3.2 18.7 - - - +
178H LEU* 3.8 3.2 - - - -
179H TYR* 2.9 56.8 + + + +
181H LEU* 3.8 13.9 - - + +
203H HIS* 3.7 2.7 - - - +
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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