Contacts of the strand formed by residues 140 - 146 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ILE* 4.0 12.2 - - - +
138B GLY 3.8 2.8 + - - -
139B SER* 1.3 76.4 - - - +
141B TRP* 1.3 68.1 + - - -
158B THR 3.2 13.2 - - - -
159B HIS* 4.2 0.2 - - - -
160B ASP 3.9 8.3 - - - -
175B MET* 3.0 31.0 + - - +
176B TRP* 3.5 8.5 - - - +
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Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASN* 3.5 44.2 - - + -
88B HIS* 3.5 24.7 - + - -
91B PHE* 3.8 20.6 - + + -
136B ILE* 3.7 5.6 - - - +
140B GLY* 1.3 76.8 - - - -
142B GLY* 1.3 60.9 + - - +
143B TRP* 3.2 40.1 - + - +
157B THR* 3.1 9.7 - - - -
158B THR* 2.8 32.0 + - - +
160B ASP 3.3 19.3 + - - -
161B GLN* 3.0 17.0 + - - -
172B GLY 4.8 0.4 - - - -
173B VAL 3.6 11.0 - - - -
174B ASP* 3.4 51.6 - - + -
176B TRP* 3.7 7.8 - - - +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 3.7 9.1 - - - -
132B THR* 5.2 2.2 - - - -
133B LEU* 3.6 21.3 - - - +
136B ILE* 3.9 6.2 - - - +
141B TRP* 1.3 75.0 - - - +
143B TRP* 1.3 61.9 + - - -
156B THR 3.7 4.7 - - - -
157B THR* 4.4 3.8 - - - -
172B GLY* 3.2 4.5 - - - -
173B VAL 2.9 34.1 + - - -
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASN* 3.4 47.8 - - - -
90B LEU* 4.1 25.6 - - + -
91B PHE 5.8 0.2 - - - -
94B ASN* 4.9 0.7 - - - -
129B PHE* 3.6 10.6 - - - -
141B TRP* 3.2 31.4 - + + +
142B GLY* 1.3 76.4 - - - -
144B LEU* 1.3 60.3 + - - +
145B VAL* 4.1 4.7 - - + -
155B ILE* 3.3 5.4 - - - -
156B THR* 2.7 52.5 + - - +
157B THR* 4.3 0.4 - - - -
158B THR* 2.9 31.3 + - + +
164B VAL* 3.4 32.5 - - + +
169B PRO* 4.3 10.8 - - + -
171B PHE* 3.6 8.1 - - - -
172B GLY* 3.3 29.2 - - - -
207B ARG* 5.6 0.2 - - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 4.4 6.7 - - + -
115B ILE* 4.1 19.3 - - + -
119B TRP* 3.9 24.9 - - + -
125B PHE* 3.9 15.0 - - + -
129B PHE* 3.9 4.2 - - + -
143B TRP* 1.3 74.4 - - - +
145B VAL* 1.3 67.1 + - - +
153B LEU* 4.1 9.9 - - + -
154B ASP 3.3 16.8 - - - +
155B ILE* 4.6 0.4 - - + -
169B PRO* 4.0 0.3 - - - +
170B VAL* 2.8 41.1 + - + -
171B PHE* 3.1 48.9 + - + +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TRP* 4.1 6.5 - - + -
144B LEU* 1.3 79.8 - - - +
146B THR* 1.3 62.6 + - - +
153B LEU* 3.3 8.8 - - - +
154B ASP* 2.8 50.9 + - + +
156B THR* 4.2 16.2 - - + +
164B VAL* 3.7 34.8 - - + -
167B ALA* 3.9 18.8 - - + -
168B ALA 3.2 14.8 - - - +
169B PRO* 3.9 5.4 - - + -
170B VAL* 4.0 5.4 - - - -
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 1.3 75.6 - - - +
147B ASP* 1.3 59.7 + - - +
148B GLY 2.7 28.7 + - - +
151B GLY* 3.1 18.7 + - - -
152B LYS 3.2 7.2 - - - -
153B LEU* 4.1 0.2 - - - -
167B ALA* 3.7 5.8 - - - +
168B ALA* 3.0 46.1 + - + +
170B VAL* 4.1 7.0 - - + -
207B ARG 4.8 0.2 - - - +
208B TYR* 3.3 29.8 - - + +
211B GLY* 4.1 7.4 - - - -
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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