Contacts of the strand formed by residues 204 - 215 (chain A) in PDB entry 1K1P
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 LYS 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.4 0.9 - - - -
122A SER* 3.6 21.1 + - - -
123A LEU 3.5 19.5 + - - +
124A PRO* 4.0 18.2 - - + -
125A THR* 4.9 19.4 - - - +
200A VAL* 3.3 6.7 - - - -
201A CYS 3.0 31.2 + - - +
202A SER* 3.9 11.9 - - - +
203A GLY* 1.3 89.0 + - - +
209A LEU* 1.3 59.7 + - - +
210A GLN* 3.1 14.1 + - - +
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Residues in contact with LEU 209 (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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45A SER* 3.7 22.0 - - - +
47A ILE* 4.5 13.9 - - + -
53A VAL* 4.7 11.7 - - + -
121A ILE* 4.0 17.4 - - + +
122A SER 2.9 19.3 + - - +
123A LEU* 4.5 10.5 - - + -
124A PRO* 2.8 24.5 - - - +
198A PRO* 3.7 27.1 - - + -
199A VAL 3.9 5.2 - - - +
200A VAL* 4.3 5.2 - - + -
204A LYS* 1.3 68.2 - - - +
210A GLN* 1.3 59.4 + - - +
211A GLY 3.6 23.1 - - - +
212A ILE* 5.3 2.9 - - + -
231A VAL* 3.7 18.5 - - + +
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Residues in contact with GLN 210 (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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124A PRO* 3.6 17.4 - - - +
127A SER 3.3 20.7 + - - +
128A CYS* 3.9 4.9 - - - +
129A ALA* 3.4 33.7 + - + +
162A ILE* 5.1 1.3 - - + +
181A PHE* 3.4 18.6 - - + -
199A VAL 2.9 5.5 + - - -
201A CYS* 3.6 42.3 - - + +
204A LYS* 3.1 14.6 + - - +
209A LEU* 1.3 74.5 - - - +
211A GLY* 1.3 58.1 + - - +
230A LYS* 4.0 1.8 - - - +
231A VAL* 3.2 22.5 + - - -
232A CYS* 4.4 6.3 + - - +
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Residues in contact with GLY 211 (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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181A PHE* 3.8 8.3 - - - -
198A PRO* 3.8 1.0 - - - +
199A VAL* 3.1 40.4 + - - +
209A LEU* 3.6 10.8 - - - +
210A GLN* 1.3 80.6 - - - +
212A ILE* 1.3 67.8 + - - +
229A THR 3.1 10.8 - - - -
231A VAL* 3.7 2.9 - - - +
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Residues in contact with ILE 212 (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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53A VAL* 3.7 31.4 - - + +
54A SER 3.7 8.1 - - - +
55A ALA* 3.7 19.7 - - + +
102A ASP 4.3 0.2 - - - +
103A ILE* 3.7 21.8 - - + -
196A GLY* 3.6 32.3 - - - +
197A GLY 3.3 4.5 - - - +
199A VAL* 4.2 0.6 - - - +
209A LEU* 5.3 4.3 - - + -
211A GLY* 1.3 79.7 - - - +
213A VAL* 1.3 68.2 + - - +
214A SER* 3.0 5.0 + - - -
228A TYR* 3.3 6.9 - - - -
229A THR* 3.1 35.3 + - - +
231A VAL* 3.7 15.5 - - + -
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Residues in contact with VAL 213 (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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55A ALA* 4.0 3.5 - - - +
57A HIS* 4.1 0.5 - - - -
138A ILE* 4.1 18.4 - - + -
139A SER 5.0 1.1 - - - +
190A SER* 3.6 26.0 - - - +
194A ASP* 3.4 33.7 - - + +
195A SER* 3.7 3.7 - - - +
196A GLY* 3.0 20.4 + - - +
197A GLY* 2.9 21.6 + - - +
198A PRO 4.5 1.1 - - - +
199A VAL* 4.6 0.2 - - + -
212A ILE* 1.3 71.1 - - - +
214A SER* 1.3 59.9 + - - +
227A VAL 5.5 0.2 - - - +
228A TYR* 3.5 19.9 - - + -
999A MEL 3.9 18.6 - - + -
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Residues in contact with SER 214 (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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55A ALA* 5.5 0.2 - - - -
57A HIS* 3.0 13.9 + - - -
99A LEU* 3.9 2.1 + - - +
102A ASP* 2.6 33.3 + - - +
180A MET* 6.5 0.2 - - - -
212A ILE 3.0 9.8 + - - -
213A VAL* 1.3 74.4 - - - +
215A TRP* 1.3 78.1 + - - +
227A VAL 3.3 13.8 + - - -
228A TYR* 4.1 0.9 - - - -
229A THR* 3.8 15.0 - - - -
999A MEL 3.0 23.9 + - - -
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Residues in contact with TRP 215 (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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98A THR 4.3 6.6 + - - -
99A LEU* 3.6 18.2 - - + -
172A TYR* 3.9 27.1 - + - -
175A GLN* 3.9 21.3 - - + -
176A ILE* 3.8 19.5 - - + -
180A MET* 3.7 24.1 - - + +
214A SER* 1.3 104.7 - - - +
216A GLY* 1.3 80.7 + - - +
227A VAL* 2.9 63.8 + - + +
999A MEL 3.0 74.2 + - + +
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Residues in contact with GLY 216 (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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172A TYR* 3.9 10.5 - - - -
215A TRP* 1.3 96.9 - - - +
217A SER* 1.3 59.7 + - - -
219A GLY 4.0 0.7 - - - -
225A PRO 4.4 4.0 - - - -
227A VAL* 4.5 0.7 - - - -
999A MEL 3.0 45.4 + - - +
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Residues in contact with SER 217 (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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172A TYR* 3.5 14.5 + - - -
216A GLY* 1.3 71.8 - - - -
219A GLY* 1.3 68.1 + - - +
220A CYS* 3.5 1.6 + - - -
221A GLN* 4.1 7.3 - - - +
224A LYS* 3.8 49.9 + - - +
999A MEL 3.4 10.6 + - - -
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Residues in contact with GLY 219 (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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217A SER* 1.3 75.6 + - - +
220A CYS* 1.3 69.1 + - - -
221A GLN* 4.6 5.8 - - - -
999A MEL 3.0 42.3 + - - +
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Residues in contact with CYS 220 (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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17A VAL* 4.2 8.7 - - + -
145A LYS 4.7 0.7 - - - +
146A SER* 3.5 15.3 + - - +
190A SER 3.9 3.6 - - - +
191A CYS* 2.0 60.1 - - + -
192A GLN* 3.9 8.3 - - - -
217A SER 3.5 1.2 + - - -
219A GLY* 1.3 85.0 - - - -
221A GLN* 1.3 92.1 + - - +
999A MEL 3.8 9.0 - - - -
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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