Contacts of the strand formed by residues 3 - 12 (chain H) in PDB entry 5U07
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 PHE 3 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2H THR* 1.3 101.7 - - - +
4H VAL* 1.3 64.1 + - - +
5H ASP* 3.4 2.5 + - - +
187H GLN* 6.1 2.9 - - - -
236H ASN* 5.5 3.1 - - + +
237H VAL 3.5 4.5 - - - +
238H ASN* 3.2 46.7 - - + -
240H ASP* 6.0 0.4 - - - -
288H VAL* 4.7 0.7 - - - -
289H ARG* 2.9 39.0 + - + +
290H PHE 4.1 6.5 - - - -
291H ASP 4.1 13.9 - - - -
292H ARG* 4.3 3.8 - - - -
293H PRO* 3.5 46.9 - - + -
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Residues in contact with VAL 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H PHE* 1.3 72.5 - - - +
5H ASP* 1.3 61.6 + - - +
6H ILE* 4.3 1.6 + - + +
235H ALA 4.0 0.7 - - - +
236H ASN* 3.5 1.6 - - - -
237H VAL* 2.8 44.9 + - + +
239H LEU* 3.6 33.4 - - + -
256H VAL* 5.1 7.2 - - + -
260H LEU* 4.2 22.7 - - + -
286H ILE* 4.1 19.5 - - + -
287H ALA 3.6 8.3 - - - +
288H VAL* 4.3 17.5 - - + +
363H MET* 5.7 2.7 - - + +
364H VAL* 5.9 4.5 - - + +
367H ALA* 4.6 4.3 - - + -
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Residues in contact with ASP 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H PHE 4.5 0.9 - - - +
4H VAL* 1.3 75.9 - - - +
6H ILE* 1.3 60.4 + - - +
7H HIS* 3.5 17.2 + - - -
234H TYR* 3.7 7.0 - - + +
235H ALA 3.3 4.3 - - - +
236H ASN* 3.1 23.6 - - - +
285H HIS 3.7 1.7 - - - +
286H ILE* 3.6 1.7 - - - +
287H ALA* 2.6 50.9 + - - +
289H ARG* 3.4 22.3 + - - +
293H PRO* 4.5 3.6 - - + -
294H ILE 3.6 16.8 + - - +
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Residues in contact with ILE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 5.5 1.3 - - + +
5H ASP* 1.3 74.0 - - - +
7H HIS* 1.3 73.1 + - - +
233H ARG 3.9 0.3 - - - +
234H TYR* 3.3 7.3 - - - -
235H ALA* 2.9 53.2 + - + +
237H VAL* 6.3 1.1 - - + -
259H PHE* 5.4 2.2 - - + -
260H LEU* 4.5 21.8 - - + +
263H PHE* 3.3 37.4 - - + -
264H LEU* 3.8 19.7 - - + -
284H VAL* 4.2 3.1 - - + -
285H HIS 3.6 3.1 - - - -
286H ILE* 3.4 28.9 - - + -
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Residues in contact with HIS 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ASP* 3.5 21.7 + - - -
6H ILE* 1.3 80.5 - - - +
8H ALA* 1.3 65.8 + - - +
232H TYR* 3.1 25.7 + - + +
233H ARG 3.4 6.3 - - - +
234H TYR* 3.5 17.3 - + - -
283H LEU* 5.4 0.9 - - + -
284H VAL* 3.4 2.8 - - - -
285H HIS* 2.9 66.4 + + + +
287H ALA* 5.1 0.2 - - - +
294H ILE 3.2 23.7 + - - -
296H PHE* 3.7 29.0 - + - -
318H LEU* 4.6 7.9 - - + -
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Residues in contact with ALA 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H HIS* 1.3 79.2 - - - +
9H ILE* 1.3 64.8 + - - +
10H GLN 4.1 0.2 - - - -
231H PHE 3.9 0.3 - - - +
232H TYR* 3.6 5.0 - - - -
233H ARG* 2.9 57.3 + - + +
263H PHE* 4.6 10.3 - - + -
264H LEU* 4.8 1.1 - - + -
281H PRO* 4.4 13.9 - - + -
283H LEU* 3.1 13.0 - - - +
284H VAL* 4.5 6.1 - - + -
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ALA* 1.3 71.7 - - - +
10H GLN* 1.3 59.3 + - - +
11H THR* 5.4 1.3 - - + +
194H VAL* 4.5 4.7 - - + -
230H THR* 4.6 15.0 - - - +
231H PHE 3.6 4.9 - - - +
232H TYR* 3.6 38.6 - - + -
281H PRO* 3.4 3.0 - - - +
282H ASP* 2.7 38.9 + - + +
283H LEU* 2.9 26.1 + - + +
300H PHE* 4.2 17.3 - - + -
311H THR* 5.5 3.8 - - - +
314H ALA* 4.6 19.1 - - + +
315H CYS* 5.0 13.5 - - - -
318H LEU* 4.3 12.8 - - + -
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Residues in contact with GLN 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 1.3 77.2 - - - +
11H THR* 1.3 70.3 + - - +
12H LEU* 3.9 11.0 + - + +
43H TRP* 3.8 9.0 - - - -
230H THR* 4.3 0.4 - - - -
231H PHE* 2.9 38.3 + - + +
233H ARG* 2.7 43.9 + - - -
264H LEU 4.7 1.7 + - - +
266H THR 5.1 0.4 + - - -
267H VAL* 3.9 17.8 - - - +
279H THR* 2.5 33.2 + - + -
280H LEU 4.2 2.2 - - - -
281H PRO* 3.3 25.5 - - + +
282H ASP 4.2 1.3 - - - +
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Residues in contact with THR 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G TYR* 4.1 13.5 + - - -
298G PRO* 3.1 28.2 - - + +
301G GLU* 5.1 3.1 - - + -
9H ILE* 5.5 1.1 - - + -
10H GLN* 1.3 75.1 - - - +
12H LEU* 1.3 64.9 + - - +
13H PRO* 4.3 0.7 - - - +
229H GLY 3.5 7.2 - - - -
230H THR* 3.6 20.2 - - + +
279H THR* 3.3 22.7 + - - +
282H ASP* 3.2 25.8 + - - +
311H THR* 3.5 20.6 - - + -
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G TYR* 4.3 3.9 - - - -
10H GLN* 4.3 16.8 - - + +
11H THR* 1.3 83.6 - - - +
13H PRO* 1.3 64.5 - - - +
14H TYR 3.9 0.2 - - - -
15H SER* 3.6 18.2 - - - +
17H ILE* 3.6 22.0 - - + -
43H TRP* 5.5 5.6 - - + -
228H ALA* 3.4 4.9 - - - +
229H GLY 2.9 34.7 + - - +
231H PHE* 3.3 35.7 - - + -
267H VAL* 5.0 7.2 - - + -
277H ALA* 3.1 31.2 - - + +
279H THR* 4.0 7.6 - - - +
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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