Contacts of the strand formed by residues 128 - 136 (chain L) 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 GLY 128 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123L GLN* 3.0 34.5 + - - +
124L LEU* 3.4 9.0 - - - +
126L SER* 3.4 4.8 - - - -
127L GLY* 1.3 81.0 - - - +
129L ALA* 1.3 62.0 + - - +
179L THR* 5.9 1.6 - - - -
180L LEU 3.9 7.2 - - - -
181L THR* 4.4 0.9 - - - -
182L LYS* 4.2 3.1 - - - -
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Residues in contact with ALA 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L PRO* 3.9 14.1 - - + -
123L GLN* 4.0 4.3 - - - +
124L LEU* 4.2 5.4 - - + -
128L GLY* 1.3 75.2 - - - +
130L SER* 1.3 60.4 + - - +
131L VAL 4.2 0.7 - - - -
179L THR* 3.4 1.8 - - - +
180L LEU* 2.8 43.6 + - + +
181L THR 4.0 7.6 - - - +
185L TYR* 3.7 38.1 - - + -
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Residues in contact with SER 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU* 5.6 2.4 - - - +
145H LEU* 3.9 16.9 - - - +
147H LYS* 4.2 5.7 - - - -
117L PHE 4.2 0.9 - - - +
118L PRO 4.6 0.5 - - - +
119L PRO* 3.7 19.7 - - - +
123L GLN* 2.8 35.4 + - - +
129L ALA* 1.3 71.8 - - - +
131L VAL* 1.3 62.9 + - - +
132L VAL* 3.7 6.5 + - - +
177L THR* 4.1 8.8 - - - +
178L LEU 3.1 5.6 - - - -
179L THR* 2.6 25.9 + - - +
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Residues in contact with VAL 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L ILE* 3.9 4.7 - - + -
117L PHE 3.4 17.0 - - - +
119L PRO* 4.3 13.5 - - + -
130L SER* 1.3 74.5 - - - +
132L VAL* 1.3 58.7 + - - +
147L TRP* 3.5 32.3 - - + -
177L THR* 3.5 2.3 - - - -
178L LEU* 2.7 39.4 + - + +
180L LEU* 4.0 22.4 - - + -
185L TYR* 4.5 3.4 - - + -
191L TYR* 4.1 19.3 - - + -
208L PHE* 3.7 22.7 - - + -
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Residues in contact with VAL 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H LEU* 3.8 27.4 - - + -
145H LEU* 4.2 22.9 - - + -
182H SER* 5.0 2.9 - - - -
115L SER 3.7 1.0 - - - +
116L ILE* 3.4 1.9 - - - +
117L PHE* 2.7 40.7 + - + +
130L SER 3.7 5.4 + - - +
131L VAL* 1.3 78.6 - - - +
133L CYS* 1.3 62.7 + - - +
134L PHE* 3.7 37.9 - - + -
147L TRP* 4.2 1.8 - - - -
175L SER* 5.0 1.8 - - - -
176L SER 3.4 7.4 - - - +
177L THR* 3.9 20.4 - - + +
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Residues in contact with CYS 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L VAL* 3.3 22.2 - - - -
115L SER 3.2 8.1 - - - -
116L ILE* 4.7 0.9 - - - -
132L VAL* 1.3 75.6 - - - +
134L PHE* 1.3 63.2 + - - +
135L LEU* 3.8 7.6 - - - +
147L TRP* 3.7 15.9 - - + -
175L SER* 3.3 3.5 - - - -
176L SER* 2.8 38.1 + - - +
193L CYS* 2.0 52.7 - - + -
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Residues in contact with PHE 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H LEU* 4.1 10.1 - - + -
141H THR* 4.3 5.4 - - + -
143H GLY* 3.7 18.4 - - - -
170H PHE* 3.7 13.5 - + - -
182H SER* 3.7 32.1 - - - -
183H SER 4.0 7.9 - - - -
184H SER* 3.5 27.6 - - - -
113L THR 3.2 6.6 - - - +
114L VAL* 3.4 0.7 - - - -
115L SER* 2.8 39.3 + - - +
117L PHE* 3.6 25.6 - + - -
132L VAL* 3.7 18.2 - - + -
133L CYS* 1.3 73.5 - - - +
135L LEU* 1.3 59.5 + - - +
136L ASN* 3.8 13.5 - - - +
174L MET 3.6 1.6 - - - -
175L SER* 3.6 15.7 - - - -
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Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L PRO* 4.2 7.6 - - + -
113L THR 3.9 6.1 - - - -
114L VAL* 4.4 7.4 - - + -
133L CYS* 3.8 28.7 - - + +
134L PHE* 1.3 77.2 - - - +
136L ASN* 1.3 60.6 + - - +
138L PHE* 3.0 19.4 - - + -
143L ILE* 3.7 20.4 - - + -
145L VAL* 4.3 22.2 - - + -
174L MET* 2.8 55.6 + - + +
176L SER* 4.7 3.1 - - - +
193L CYS* 4.5 2.0 - - - -
195L ALA* 3.7 30.3 - - + -
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Residues in contact with ASN 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H THR* 5.1 4.9 - - - +
168H HIS* 3.4 10.7 + - + -
170H PHE* 3.5 16.8 - - - -
184H SER* 3.2 24.6 + - - -
186H THR* 5.4 3.1 + - - -
112L PRO* 3.6 1.0 - - - +
113L THR* 3.0 37.3 + - - +
134L PHE* 4.2 9.5 - - - +
135L LEU* 1.3 88.1 + - - +
137L ASN* 1.3 84.2 + - - +
138L PHE* 3.6 3.1 - - - -
173L SER* 3.2 21.2 + - - +
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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