Contacts of the strand formed by residues 30 - 36 (chain B) in PDB entry 5FA5
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 GLN 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.8 18.5 - - + -
62A ARG* 5.1 5.3 - - - +
28B GLU 3.4 0.2 - - - -
29B ARG* 1.3 96.9 - - - +
31B LEU* 1.4 65.4 + - - +
32B GLU* 3.3 5.4 + - - +
46B ALA* 4.4 1.8 - - - -
47B SER* 3.0 35.1 + - - +
48B SER* 3.9 3.1 - - - -
49B LEU* 3.1 46.4 + - + -
50B SER* 4.3 5.8 + - - -
318B TRP* 3.5 40.1 + - + +
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Residues in contact with LEU 31 (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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27B MET* 3.6 24.5 - - - -
28B GLU 4.0 0.2 - - - +
29B ARG 3.3 1.6 + - - -
30B GLN* 1.4 67.4 - - - +
32B GLU* 1.3 59.4 + - - +
33B ALA 3.8 1.1 - - - +
44B LEU* 5.0 7.6 - - + -
45B GLY 3.7 6.1 - - - +
46B ALA* 4.0 10.8 - - + -
68B PRO* 4.5 2.9 - - + -
301B ARG* 3.3 24.9 - - - +
316B VAL* 3.8 23.5 - - + +
317B GLY* 3.5 15.8 + - - +
318B TRP* 3.5 3.0 - - - -
320B HIS* 3.5 42.2 - - + +
321B GLN 3.9 2.5 - - - +
322B VAL* 3.7 29.8 - - + -
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Residues in contact with GLU 32 (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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49A ARG* 3.7 15.5 + - - -
30B GLN 3.3 6.2 + - - +
31B LEU* 1.3 73.3 - - - +
33B ALA* 1.3 58.1 + - + +
45B GLY 2.8 15.8 + - - +
47B SER* 4.6 2.4 + - - +
49B LEU* 5.0 0.7 - - - +
83B VAL* 3.4 28.0 - - + +
84B ALA 3.5 22.2 - - - +
85B ASP* 4.5 2.2 - - - +
259B THR* 5.6 0.3 - - - +
301B ARG* 3.0 53.0 + - - +
302B ASP* 3.6 9.0 - - - +
316B VAL* 4.4 0.7 - - - -
318B TRP* 3.1 27.0 + - - -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.8 0.7 - - - +
32B GLU* 1.3 82.7 - - + +
34B ALA* 1.3 60.3 + - - +
35B ARG* 3.9 5.4 - - - +
43B LEU 4.2 1.1 - - - -
44B LEU* 3.4 12.0 - - - +
45B GLY* 3.1 26.5 + - - +
83B VAL* 5.4 0.9 - - + -
85B ASP* 5.2 3.1 - - - +
86B LEU* 3.6 41.5 - - + +
302B ASP* 3.3 12.3 - - - +
316B VAL* 3.9 5.2 - - - +
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Residues in contact with ALA 34 (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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33B ALA* 1.3 74.5 - - - +
35B ARG* 1.3 66.3 + - - +
42B LEU* 4.3 4.7 - - + -
43B LEU 3.2 7.2 - - - -
44B LEU* 3.9 6.1 - - + -
302B ASP* 2.8 28.5 + - + +
303B ALA 4.0 0.2 - - - +
304B THR* 3.3 27.1 - - + -
314B THR* 5.0 3.8 - - + +
316B VAL* 3.7 28.5 - - + -
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Residues in contact with ARG 35 (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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33B ALA* 3.9 7.7 - - - +
34B ALA* 1.3 85.4 - - - +
36B TYR* 1.3 58.9 + - - +
42B LEU* 3.8 2.6 - - - +
43B LEU* 2.9 37.8 + - + +
85B ASP* 3.7 17.6 + - - -
86B LEU* 2.8 45.3 + - + +
87B THR* 4.3 15.6 + - - +
88B TRP* 3.1 30.0 + - + +
131B VAL 5.0 3.2 + - - -
302B ASP* 2.7 35.0 + - - -
303B ALA 5.2 2.0 - - - -
304B THR* 3.5 9.1 - - - +
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Residues in contact with TYR 36 (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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35B ARG* 1.3 73.7 - - - +
37B ARG* 1.3 60.5 + - - +
40B GLY* 3.5 19.3 - - - -
41B ALA 3.4 5.4 - - - -
42B LEU* 3.9 13.5 - - + -
64B PRO* 3.8 29.5 - - + +
88B TRP* 3.9 7.8 - - - -
304B THR* 3.0 42.4 + - + +
305B TRP 3.6 17.3 - - - +
306B SER* 3.7 17.9 - - - -
307B PRO* 3.7 22.8 - - + +
312B LEU* 4.1 7.2 - - - +
314B THR* 2.7 33.2 + - - -
324B HIS* 3.7 10.6 + - - -
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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