Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 1KKC
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ILE* 4.0 11.5 - - - +
138A GLY 3.8 2.6 + - - -
139A SER* 1.3 76.2 - - - +
141A TRP* 1.3 68.7 + - - -
158A THR 3.3 12.6 - - - -
159A HIS* 4.3 0.2 - - - -
160A ASP 3.9 8.5 - - - -
175A MET* 2.9 30.1 + - - +
176A TRP* 3.5 9.2 + - - +
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Residues in contact with TRP 141 (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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87A ASN* 3.5 36.0 - - + +
88A HIS* 3.6 17.9 - + - -
91A PHE* 3.7 35.2 - + + -
136A ILE* 3.5 7.2 - - - +
140A GLY* 1.3 75.7 - - - -
142A GLY* 1.3 59.8 + - - +
143A TRP* 3.2 40.4 - + - +
157A THR* 3.1 10.4 - - - -
158A THR* 2.9 32.9 + - - +
160A ASP 3.4 18.0 + - - -
161A GLN* 3.0 19.4 + - - -
172A GLY 4.5 0.4 - - - -
173A VAL 3.6 11.0 - - - -
174A ASP* 3.5 56.5 + - + -
176A TRP* 3.9 1.4 - - - +
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Residues in contact with GLY 142 (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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129A PHE* 3.6 9.7 - - - -
132A THR* 5.4 1.8 - - - -
133A LEU* 3.4 24.1 - - - +
136A ILE* 4.2 3.6 - - - -
141A TRP* 1.3 73.4 - - - +
143A TRP* 1.3 62.0 + - - -
156A THR 3.6 4.9 - - - -
157A THR* 4.4 3.4 - - - -
172A GLY* 3.4 3.6 - - - -
173A VAL 3.0 33.1 + - - -
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Residues in contact with TRP 143 (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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87A ASN* 3.4 44.2 - - + -
90A LEU* 4.1 24.5 - - + -
91A PHE 5.8 0.2 - - - -
94A ASN* 5.1 0.2 - - - -
129A PHE* 3.6 12.9 - - - -
141A TRP* 3.2 39.7 - + + +
142A GLY* 1.3 76.6 - - - -
144A LEU* 1.3 58.5 + - - +
145A VAL* 3.9 9.9 - - + -
155A ILE* 3.2 5.9 - - - +
156A THR* 2.6 52.3 + - - +
158A THR* 2.8 32.8 + - + +
162A ASP 5.1 0.4 - - - -
164A VAL* 3.4 24.9 - - + -
169A PRO* 4.3 9.9 - - + -
171A PHE* 3.6 8.7 - - - -
172A GLY* 3.3 28.9 - - - -
207A ARG* 5.9 0.2 - - - -
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Residues in contact with LEU 144 (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 LEU* 4.3 5.6 - - + -
115A ILE* 4.1 19.5 - - + -
119A TRP* 4.0 15.9 - - + -
125A PHE* 3.8 23.6 - - + -
129A PHE* 3.8 6.8 - - + -
143A TRP* 1.3 72.8 - - - +
145A VAL* 1.3 62.7 + - - +
153A LEU* 4.0 15.7 - - + -
154A ASP 3.5 12.8 - - - +
155A ILE* 4.5 0.9 - - + +
169A PRO* 3.9 0.5 - - - +
170A VAL* 2.9 41.4 + - + +
171A PHE* 3.1 48.2 + - + +
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Residues in contact with VAL 145 (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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143A TRP* 3.9 18.2 - - + -
144A LEU* 1.3 80.1 - - - +
146A THR* 1.3 61.8 + - - +
152A LYS 3.8 0.2 - - - +
153A LEU* 3.3 6.9 - - - +
154A ASP* 2.8 51.8 + - + +
156A THR* 4.0 17.0 - - + +
164A VAL* 3.8 26.2 - - + -
167A ALA* 4.0 19.5 - - + -
168A ALA 3.3 13.0 - - - +
169A PRO* 4.1 2.9 - - + -
170A VAL* 3.9 6.1 - - - -
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Residues in contact with THR 146 (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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145A VAL* 1.3 77.2 - - - +
147A ASP* 1.3 59.9 + - - +
148A GLY 2.8 28.8 + - - +
151A GLY 3.2 19.2 + - - -
152A LYS 3.3 5.6 - - - -
153A LEU* 4.2 0.9 - - - -
167A ALA* 3.6 6.0 - - - +
168A ALA* 2.9 52.6 + - + +
170A VAL* 4.3 5.6 - - + -
207A ARG 4.8 0.7 - - - +
208A TYR* 3.4 27.5 - - + +
211A GLY* 3.9 7.6 - - - -
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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