Contacts of the strand formed by residues 257 - 264 (chain B) in PDB entry 1UMD
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 VAL 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 4.0 0.6 - - - +
206B THR* 3.2 14.8 - - - +
208B ILE* 3.5 34.5 - - + -
251B VAL* 4.1 19.5 - - + -
256B ARG* 1.3 77.7 - - - +
258B VAL* 1.3 71.5 + - - +
259B LEU* 4.0 8.3 - - + -
277B ILE* 4.2 15.5 - - + -
285B LEU* 4.6 4.9 - - + -
287B ALA 5.4 0.4 + - - -
288B PRO 3.9 5.2 + - - +
289B PRO* 3.7 24.5 - - + +
290B ILE* 3.1 23.2 + - - +
321B ALA* 4.9 1.9 - - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.2 6.5 - - + -
206B THR 2.9 5.3 + - - -
207B LEU* 3.4 21.4 - - + +
208B ILE 3.0 23.4 + - - +
257B VAL* 1.3 78.3 - - - +
259B LEU* 1.3 64.1 + - - +
260B VAL* 4.0 13.3 + - + +
290B ILE* 3.2 14.1 - - + +
292B VAL* 3.9 24.7 - - + -
314B ILE* 4.9 3.6 - - + +
317B ALA* 3.8 31.0 - - + +
318B ALA* 4.0 9.4 - - - -
321B ALA* 4.1 9.9 - - + -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 3.3 24.5 - - + +
257B VAL* 4.0 21.5 - - + +
258B VAL* 1.3 74.6 - - - +
260B VAL* 1.3 63.3 + - - +
270B VAL* 3.7 34.5 - - + +
273B VAL* 3.6 33.2 - - + -
274B ALA* 3.8 19.5 - - + +
277B ILE* 4.4 1.1 - - + -
289B PRO* 4.5 2.2 - - + -
290B ILE 2.8 26.8 + - - +
291B ARG* 3.5 5.4 - - + +
292B VAL* 2.8 27.4 + - - +
293B THR* 5.0 1.0 - - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 4.9 4.3 - - + -
208B ILE 2.8 15.0 + - - +
209B CYS* 3.5 19.1 - - - -
210B TYR* 4.2 2.6 + - - -
213B VAL* 3.6 26.6 - - + +
217B VAL* 3.9 24.0 - - + -
258B VAL* 4.0 20.2 - - + +
259B LEU* 1.3 80.1 - - - +
261B SER* 1.3 68.6 + - - +
270B VAL* 4.2 5.3 - - - +
292B VAL* 3.3 20.6 - - + +
309B PRO* 4.2 3.1 - - + -
314B ILE* 4.0 22.7 - - + -
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Residues in contact with SER 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU* 3.9 1.6 + - - -
210B TYR* 3.0 27.8 + - - -
213B VAL* 3.7 12.8 - - - -
260B VAL* 1.3 78.5 - - - +
262B ASP* 1.3 61.2 + - - +
263B ALA* 3.2 19.7 + - - +
268B SER* 6.4 0.2 - - - -
270B VAL* 3.7 27.1 - - - +
292B VAL 3.1 5.2 + - - +
293B THR* 3.1 26.2 - - - -
294B GLY 3.3 0.2 + - - -
309B PRO* 3.6 3.3 - - - +
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Residues in contact with ASP 262 (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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120B GLY* 3.5 0.3 - - - -
121B GLY* 3.0 30.7 + - - -
130B SER 4.2 2.1 - - - +
132B SER* 2.7 26.6 + - - -
134B GLU* 4.8 1.2 - - - +
210B TYR* 6.0 0.5 - - - -
212B THR* 3.7 18.6 + - - -
213B VAL* 3.6 7.2 - - + +
261B SER* 1.3 76.1 + - - +
263B ALA* 1.3 64.6 + - - +
264B PRO* 3.8 1.0 - - - +
294B GLY* 3.4 2.6 - - - +
299B TYR* 4.5 4.7 - - + -
307B TYR* 3.4 24.0 + - + -
308B LEU* 3.8 24.2 - - + +
309B PRO* 3.9 12.1 - - + -
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Residues in contact with ALA 263 (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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132B SER* 3.5 21.3 - - - +
134B GLU* 3.7 14.8 - - + +
135B ALA* 6.0 1.1 - - + +
210B TYR* 4.5 1.8 - - - +
261B SER* 3.2 14.7 + - - +
262B ASP* 1.3 80.6 + - - +
264B PRO* 1.3 80.3 - - + +
265B ARG 3.4 0.2 + - - -
268B SER* 4.8 7.6 - - - -
269B PHE 5.9 0.7 - - - +
293B THR* 3.5 7.3 - - - +
294B GLY 3.0 15.0 + - - -
139D HIS* 4.8 5.4 - - + -
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Residues in contact with PRO 264 (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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132B SER* 4.2 9.6 - - - +
262B ASP 3.8 1.1 - - - +
263B ALA* 1.3 84.5 - - + +
265B ARG* 1.3 66.7 + - - +
268B SER* 3.0 19.9 - - - -
294B GLY 3.7 7.2 - - - +
295B PHE 3.8 11.0 - - - +
296B ASP* 4.1 9.4 - - - +
297B THR 4.8 6.5 - - - +
307B TYR* 3.7 13.7 - - - +
139D HIS* 3.3 40.8 - - + +
141D ALA* 6.0 2.2 - - + +
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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
------------------------------------------------------------
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