Contacts of the strand formed by residues 185 - 194 (chain B) in PDB entry 3KDM
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 TYR 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B PRO* 6.0 1.7 - - - +
153B ASP* 3.0 24.1 + - - -
154B TYR* 2.9 54.4 + + + +
155B PHE* 3.7 26.5 - + - -
157B GLU* 4.3 24.0 - - + +
177B ALA* 3.5 25.4 - - + -
178B VAL 3.6 3.1 - - - -
179B LEU* 3.5 42.6 - - + +
180B GLN* 3.4 0.2 + - - -
184B LEU* 1.3 72.1 - - - +
186B SER* 1.3 60.6 + - - +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 5.9 0.9 - - - +
150B LEU* 3.9 14.7 - - - +
151B VAL 3.3 13.1 + - - -
152B LYS* 3.7 14.5 + - - +
154B TYR* 4.2 1.6 - - - -
176B PRO 4.5 0.5 - - - +
177B ALA* 4.5 0.9 - - - -
178B VAL* 3.1 31.4 + - - +
180B GLN* 3.5 27.3 + - - -
185B TYR* 1.3 77.6 - - - +
187B LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER* 6.5 0.4 - - - -
150B LEU* 3.6 6.1 - - - +
151B VAL* 2.7 60.8 + - + +
154B TYR* 3.5 22.4 - - - +
157B GLU* 5.0 1.3 - - - +
159B VAL* 4.1 12.1 - - + -
161B VAL* 4.3 7.9 - - + -
174B THR* 4.1 17.9 - - + -
175B PHE* 3.4 24.9 - - + +
176B PRO 4.2 2.9 - - - +
177B ALA* 3.9 13.9 - - + +
186B SER* 1.3 77.2 + - - +
188B SER* 1.3 71.9 + - - +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.2 13.1 - - - +
180A SER* 5.1 8.1 + - - -
182A THR* 5.1 2.3 + - - -
133B LEU* 3.6 23.1 - - - +
149B CYS 3.3 8.1 - - - -
150B LEU* 3.3 23.0 - - - +
175B PHE* 3.0 43.9 + - - +
187B LEU* 1.3 77.9 - - - +
189B SER* 1.3 61.3 + - - +
190B VAL* 4.6 3.6 - - - -
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLY* 3.0 3.3 - - - -
149B CYS 2.9 34.4 + - - +
151B VAL* 5.6 0.2 - - - -
161B VAL* 3.8 27.9 - - - +
163B TRP* 2.9 27.7 + - - -
172B VAL* 3.9 1.6 - - - +
173B HIS 3.4 5.2 - - - -
174B THR* 2.8 26.6 + - - +
187B LEU* 4.3 0.6 - - - +
188B SER* 1.3 75.1 - - - +
190B VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 190 (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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122A PHE* 4.7 8.3 - - + -
137A VAL* 5.7 1.8 - - + -
139A LEU* 3.9 33.2 - - + -
141A ASN* 4.9 1.3 - - - +
133B LEU* 4.3 17.9 - - + -
147B LEU 3.3 11.0 - - - +
148B GLY* 4.0 0.2 - - - -
163B TRP* 4.7 1.1 - - - -
171B SER 5.6 0.2 - - - +
172B VAL* 3.4 6.2 - - - +
173B HIS* 2.9 59.2 + - + +
175B PHE* 3.8 19.7 - - + -
188B SER* 4.6 3.8 - - - -
189B SER* 1.3 80.8 + - - +
191B VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 191 (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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146B ALA* 3.4 3.1 - - - +
147B LEU* 2.8 69.6 + - + +
163B TRP* 4.2 17.5 - - + -
168B LEU* 4.2 13.0 - - + -
170B SER 3.6 22.9 - - - +
171B SER 3.7 5.4 - - - +
172B VAL* 3.8 17.3 - - + -
190B VAL* 1.3 76.8 - - - +
192B THR* 1.3 72.2 + - - +
193B VAL* 4.2 11.2 - - + -
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Residues in contact with THR 192 (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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120A PHE* 4.4 4.9 - - + -
139A LEU* 4.8 1.6 - - + -
141A ASN* 3.9 32.4 + - - +
142A ASN* 5.2 3.3 + - - -
144B THR* 4.0 17.3 - - + -
145B ALA 3.3 11.4 - - - +
146B ALA* 4.0 15.0 - - + -
170B SER 4.5 0.5 - - - +
171B SER* 3.7 33.4 + - - +
190B VAL* 6.1 0.4 - - + -
191B VAL* 1.3 79.4 - - - +
193B VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 3.6 6.7 - - - +
145B ALA* 3.0 29.4 + - + +
147B LEU* 4.1 14.6 - - + -
168B LEU* 4.7 5.6 - - + -
191B VAL* 4.2 16.2 - - + -
192B THR* 1.3 81.0 - - - +
194B PRO* 1.3 87.0 - - + +
197B SER* 4.5 0.7 - - - -
198B LEU* 4.5 7.9 - - + -
203B TYR* 3.6 43.7 - - + +
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Residues in contact with PRO 194 (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 GLY 4.1 6.1 - - - +
144B THR* 4.8 2.5 - - - +
193B VAL* 1.3 93.2 - - + +
195B SER* 1.3 62.4 + - - +
196B SER* 4.2 10.8 - - - +
197B SER* 2.8 43.1 + - - +
198B LEU 4.0 0.3 + - - -
203B TYR* 5.1 0.2 - - - +
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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