Contacts of the strand formed by residues 3 - 12 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2I THR* 1.3 91.8 - - - +
4I VAL* 1.3 64.5 + - - +
5I ASP* 3.4 3.0 + - + +
187I GLN* 6.6 0.2 - - - -
236I ASN* 5.5 4.7 - - + +
237I VAL 3.6 3.8 - - - -
238I ASN* 3.5 43.1 - - + -
288I VAL* 4.6 0.7 - - - -
289I ARG* 2.9 41.9 + - + +
290I PHE 4.0 7.4 - - - -
291I ASP 3.8 15.7 - - - -
292I ARG* 4.1 3.4 - - - -
293I PRO* 3.7 41.3 - - + -
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Residues in contact with VAL 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I THR 3.9 0.2 - - - -
3I PHE* 1.3 72.4 - - - +
5I ASP* 1.3 61.1 + - - +
6I ILE* 4.3 8.5 + - + +
235I ALA 4.1 0.5 - - - +
236I ASN* 3.6 0.9 - - - -
237I VAL* 2.8 47.6 + - + +
239I LEU* 4.1 24.5 - - + -
256I VAL* 5.1 11.4 - - + -
260I LEU* 4.5 14.6 - - + -
286I ILE* 3.8 25.4 - - + -
287I ALA 3.6 4.5 - - - +
288I VAL* 4.2 18.2 - - + +
363I MET 6.0 0.4 - - - +
364I VAL* 5.5 6.1 - - + -
367I ALA* 4.7 7.0 - - + -
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Residues in contact with ASP 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I PHE 3.4 1.3 + - - -
4I VAL* 1.3 73.4 - - - +
6I ILE* 1.3 64.7 + - - +
7I HIS* 3.5 17.8 + - - -
234I TYR* 3.4 16.0 + - + +
235I ALA 3.3 3.1 - - - -
236I ASN* 3.0 25.4 - - - +
285I HIS 4.0 1.0 - - - +
286I ILE* 3.5 1.2 - - - +
287I ALA* 2.6 53.3 + - - +
289I ARG* 3.6 21.5 + - - +
293I PRO* 4.7 3.4 - - + -
294I ILE 3.6 13.8 + - - +
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Residues in contact with ILE 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL* 4.4 6.1 - - + +
5I ASP* 1.3 77.6 - - - +
7I HIS* 1.3 64.2 + - - +
234I TYR* 3.4 4.4 - - - -
235I ALA* 2.9 42.1 + - + +
237I VAL* 6.1 1.6 - - + -
259I PHE* 5.4 3.6 - - + -
260I LEU* 4.0 26.9 - - + -
263I PHE* 3.2 50.0 - - + -
264I LEU* 5.0 3.4 - - + -
284I VAL* 5.4 1.6 - - + -
285I HIS 3.7 4.0 - - - -
286I ILE* 3.4 34.1 - - + +
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Residues in contact with HIS 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ASP* 3.5 20.7 + - - -
6I ILE* 1.3 76.5 - - - +
8I ALA* 1.3 66.7 + - - +
232I TYR* 2.6 31.2 + - + +
233I ARG 3.5 5.4 - - - -
234I TYR* 3.2 17.6 - + - -
283I LEU* 5.7 0.9 - - + -
284I VAL* 3.5 5.2 - - - +
285I HIS* 2.8 65.6 + + + +
287I ALA* 5.2 0.8 - - - +
289I ARG* 5.6 0.8 + - - -
294I ILE 3.2 24.1 + - - -
296I PHE* 3.6 28.9 - + - -
318I LEU* 4.7 7.2 - - + -
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Residues in contact with ALA 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ILE* 5.0 0.2 - - + -
7I HIS* 1.3 80.2 - - - +
9I ILE* 1.3 61.2 + - - +
10I GLN* 5.6 0.2 - - + -
232I TYR* 3.7 6.5 - - - -
233I ARG* 2.8 39.4 + - + +
263I PHE* 4.0 25.4 - - + -
264I LEU* 4.5 0.9 - - + -
281I PRO* 4.5 9.0 - - + -
283I LEU* 3.1 14.8 - - - +
284I VAL* 3.9 13.2 - - + -
318I LEU* 5.9 0.9 - - - -
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Residues in contact with ILE 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I ALA* 1.3 72.5 - - - +
10I GLN* 1.3 67.5 + - - +
11I THR* 5.5 2.5 - - + -
194I VAL* 3.7 20.9 - - + -
230I THR* 4.2 15.3 - - + -
231I PHE 3.6 10.8 - - - +
232I TYR* 4.6 6.7 - - + +
281I PRO* 3.6 1.1 - - - +
282I ASP* 2.9 28.5 + - + -
283I LEU* 2.9 40.9 + - + +
300I PHE* 5.2 4.5 - - + -
311I THR* 5.5 3.8 - - + +
314I ALA* 3.3 33.2 - - + -
315I CYS* 4.7 11.0 - - - +
318I LEU* 5.7 5.6 - - + +
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Residues in contact with GLN 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I ALA* 4.1 1.3 + - + -
9I ILE* 1.3 77.6 - - - +
11I THR* 1.3 72.3 + - - +
12I LEU* 3.5 24.5 + - + +
230I THR* 4.3 0.2 - - - -
231I PHE* 2.9 35.3 + - - +
233I ARG* 2.2 45.2 + - - +
264I LEU 4.6 1.2 - - - +
266I THR 4.7 1.4 + - - -
267I VAL* 3.7 12.1 - - - +
279I THR 3.1 25.9 + - - -
280I LEU 4.4 1.8 - - - +
281I PRO* 3.1 36.6 - - + +
282I ASP 4.1 0.9 - - - +
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Residues in contact with THR 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ILE* 5.5 2.0 - - + -
10I GLN* 1.3 76.7 - - - +
12I LEU* 1.3 72.1 + - - +
13I PRO* 4.8 3.3 - - - +
229I GLY 3.3 8.5 - - - -
230I THR* 3.4 30.5 - - + +
279I THR* 3.5 19.5 - - - +
282I ASP* 3.0 29.7 + - + +
311I THR* 3.9 11.9 - - + -
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Residues in contact with LEU 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I GLN* 3.5 31.9 - - + +
11I THR* 1.3 84.3 - - - +
13I PRO* 1.3 65.2 - - + +
15I SER* 2.9 27.0 + - - +
17I ILE* 5.0 7.4 - - + -
38I VAL* 5.6 2.7 - - + -
228I ALA* 3.2 7.5 - - - +
229I GLY 2.8 32.7 + - - +
231I PHE* 3.5 35.4 - - + -
233I ARG* 5.9 3.4 - - - +
267I VAL* 4.6 16.2 - - + -
268I PRO* 5.6 4.7 - - + -
279I THR* 4.2 10.8 - - - +
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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