Contacts of the strand formed by residues 309 - 317 (chain A) in PDB entry 5UM4
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 THR 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLU* 5.8 10.1 - - + +
301A GLY 3.8 8.3 - - - +
302A ILE* 5.9 3.4 - - + -
307A GLY 5.2 2.2 - - - +
308A MET* 1.3 75.1 - - - +
310A CME 1.3 66.1 - - - +
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Residues in contact with CME 310 (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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218A LEU* 3.8 22.7 - - - -
221A SER* 3.3 26.6 + - - +
223A MET* 3.4 23.8 - - + +
300A GLU* 3.3 5.2 - - - +
301A GLY 3.1 29.9 + - - +
303A VAL* 4.4 14.4 - - + -
308A MET 4.8 0.9 - - - +
309A THR* 1.3 79.7 - - - +
311A GLN* 1.3 76.3 + - - +
312A ALA* 5.8 0.2 - - - -
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Residues in contact with GLN 311 (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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229A ARG* 4.4 1.8 - - - +
298A ILE* 3.5 20.5 - - + +
299A LEU 3.2 10.1 - - - +
300A GLU* 2.8 35.1 + - + +
310A CME 1.3 89.4 - - - +
312A ALA* 1.3 61.9 + - - +
313A ARG* 3.0 43.4 + - + +
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Residues in contact with ALA 312 (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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195A MET* 4.0 34.5 - - + -
196A PHE* 3.5 10.9 - - + -
218A LEU* 4.3 16.8 - - + -
299A LEU* 2.8 39.2 + - + +
310A CME 4.2 1.7 + - - -
311A GLN* 1.3 72.6 - - - +
313A ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 313 (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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196A PHE* 3.5 8.7 - - - -
296A VAL* 5.3 6.3 - - + -
297A VAL 3.0 13.0 - - - +
298A ILE* 4.0 18.2 - - + -
311A GLN* 3.0 41.8 + - + +
312A ALA* 1.3 79.8 - - - +
314A THR* 1.3 65.8 + - - +
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Residues in contact with THR 314 (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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196A PHE* 3.3 40.0 - - + +
197A SER 5.2 1.7 + - - -
296A VAL* 3.4 9.7 - - - +
297A VAL* 2.9 45.2 + - + -
313A ARG* 1.3 76.5 - - - +
315A SER* 1.3 72.4 + - - +
316A TYR* 3.8 17.9 - - + +
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Residues in contact with SER 315 (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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198A GLU 5.2 1.0 - - - +
294A GLU* 2.6 38.6 + - - +
295A VAL 3.3 4.7 + - - -
296A VAL* 4.4 4.5 - - - +
314A THR* 1.3 85.6 + - - +
316A TYR* 1.3 70.9 + - - +
317A THR* 4.2 2.5 + - - +
320A GLU* 3.8 7.6 - - - +
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Residues in contact with TYR 316 (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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196A PHE* 3.7 10.9 - - - +
197A SER* 3.1 29.6 + - - -
198A GLU 3.7 11.4 - - - -
199A HIS 3.6 15.9 - - - -
200A ALA* 3.6 21.1 - - + -
213A PHE* 3.4 34.0 - + + +
293A PHE* 4.6 2.3 - - - -
294A GLU* 3.3 2.2 - - - -
295A VAL* 2.7 64.1 + - + +
297A VAL* 3.7 22.7 - - + -
314A THR* 3.8 10.1 - - + -
315A SER* 1.3 78.3 + - - +
317A THR* 1.3 67.4 + - - +
320A GLU* 3.6 8.5 - - + -
321A VAL* 4.3 12.3 - - + -
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Residues in contact with THR 317 (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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293A PHE* 3.6 11.4 - - - +
294A GLU* 3.7 27.8 - - - +
315A SER* 4.2 1.8 - - - +
316A TYR* 1.3 74.8 - - - +
318A GLU* 1.3 65.0 + - - +
319A ASP* 2.8 22.1 + - - -
320A GLU* 2.8 43.6 + - - +
321A VAL* 3.4 10.1 + - - +
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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