Contacts of the strand formed by residues 118 - 127 (chain F) in PDB entry 3A13
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 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F VAL* 4.0 15.0 - - + -
32F THR 3.4 9.9 - - - +
34F ALA* 3.7 5.6 - - - +
42F ALA* 4.0 20.9 - - + +
45F ALA* 6.2 0.2 - - + -
46F VAL* 4.4 15.9 - - + -
112F ILE 4.2 17.7 - - - +
113F PHE 5.0 4.5 - - - +
115F MET* 3.2 24.8 - - + +
116F LYS* 3.1 4.2 - - - +
117F ARG* 1.3 86.6 - - + +
119F LYS* 1.3 60.5 + - - +
120F GLY 4.0 10.1 - - - +
121F LEU* 4.4 12.8 - - + +
294F HIS* 6.0 0.4 - - + -
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F THR* 2.8 22.2 + - + +
33F PRO 3.8 17.9 - - - +
34F ALA* 3.8 6.8 - - + +
35F GLU* 4.8 19.5 + - - +
118F VAL* 1.3 74.8 - - - +
120F GLY* 1.3 56.4 + - - +
294F HIS* 4.6 5.3 - - - +
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Residues in contact with GLY 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG 4.3 0.7 - - - -
31F VAL* 3.8 1.9 - - - -
32F THR* 2.9 36.2 + - - +
118F VAL* 3.3 6.2 - - - +
119F LYS* 1.3 82.1 - - - +
121F LEU* 1.3 61.1 + - - +
293F TYR* 3.3 18.4 - - - -
294F HIS* 3.6 9.4 - - - -
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F PHE* 3.4 38.6 - - + -
30F ARG 3.5 1.3 - - - -
31F VAL* 3.9 17.9 - - + -
46F VAL* 4.2 15.5 - - + -
112F ILE* 3.4 55.2 - - + +
113F PHE* 3.3 25.0 - - + +
115F MET* 4.7 0.2 - - + -
118F VAL* 4.4 10.1 - - + -
120F GLY* 1.3 74.6 - - - +
122F ARG* 1.3 59.8 + - - +
293F TYR 3.2 1.0 + - - -
294F HIS* 3.0 15.2 - - + +
295F GLY 3.0 17.5 + - - -
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Residues in contact with ARG 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F PHE* 3.2 5.4 - - - -
30F ARG* 2.7 43.4 + - + -
121F LEU* 1.3 74.1 - - - +
123F LEU* 1.3 63.8 + - - +
124F GLU* 3.0 33.7 + - - +
288F PHE 4.9 0.2 + - - -
289F THR* 3.0 29.3 + - - +
290F ARG 4.9 0.2 - - - -
291F ASN 3.4 18.7 + - - -
292F PRO* 3.2 28.9 + - - +
293F TYR 3.9 4.0 + - - -
294F HIS 3.7 11.9 - - - +
295F GLY 3.4 11.0 - - - +
296F ILE 4.1 1.2 + - - -
297F SER* 3.1 38.4 + - - +
298F MET 4.6 1.0 - - - +
329F ILE* 4.6 18.6 - - - +
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Residues in contact with LEU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA* 4.2 12.6 - - + -
28F VAL 3.6 9.4 - - - +
29F PHE* 4.0 23.8 - - + -
105F LEU* 5.8 0.9 - - + -
108F ILE* 3.8 31.0 - - + +
109F ALA* 4.2 9.0 - - + -
113F PHE* 4.4 7.2 - - + -
121F LEU 4.1 0.8 + - - -
122F ARG* 1.3 69.8 - - - +
124F GLU* 1.3 58.8 + - - +
125F ASP 3.2 25.1 - - - +
126F LEU* 4.3 4.7 - - + -
295F GLY 3.1 13.2 + - - +
296F ILE* 4.4 10.1 - - + -
297F SER* 2.9 27.4 + - - -
300F VAL* 3.8 26.3 - - + +
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Residues in contact with GLU 124 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28F VAL* 2.7 19.3 + - + +
29F PHE 4.4 2.2 - - - -
30F ARG* 3.6 25.0 + - + +
86F ILE* 4.7 0.9 - - + -
122F ARG* 3.0 51.3 + - - +
123F LEU* 1.3 72.6 - - - +
125F ASP* 1.3 59.1 + - - +
292F PRO 4.0 0.5 - - - +
297F SER* 3.9 10.9 + - - -
299F PHE* 3.9 6.6 - - - +
300F VAL* 3.6 8.3 - - - +
350F PHE* 3.5 53.7 - - + +
351F HIS* 3.9 14.6 + - - -
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Residues in contact with ASP 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ILE 4.3 0.4 - - - -
27F ALA* 3.6 0.7 - - - -
28F VAL* 3.0 34.9 + - + -
123F LEU* 3.2 12.1 - - - +
124F GLU* 1.3 80.7 - - - +
126F LEU* 1.3 83.8 + - - +
127F TYR 4.2 1.3 - - - -
299F PHE* 3.6 21.7 - - - -
300F VAL* 3.5 10.4 - - - +
303F LYS* 3.0 25.8 + - - +
350F PHE 3.6 14.6 - - - +
351F HIS* 3.4 5.2 - - - -
352F LEU* 3.0 31.6 + - - +
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ILE* 4.6 7.9 - - + -
26F ILE 3.5 2.9 - - - +
27F ALA* 3.9 23.6 - - + +
104F LEU* 4.7 2.0 - - + -
105F LEU* 4.6 3.8 - - + -
108F ILE* 3.8 32.3 - - + -
123F LEU* 4.3 4.5 - - + -
125F ASP* 1.3 95.4 + - - +
127F TYR* 1.3 57.7 + - - +
128F PHE* 3.7 31.9 + - + -
300F VAL* 4.1 15.5 - - + +
303F LYS* 2.6 37.1 + - + +
304F LEU* 4.4 23.3 - - + -
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Residues in contact with TYR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F SER 5.0 0.2 - - - -
21F LYS* 2.6 40.3 + - + +
24F ASP 3.3 22.9 - - - -
25F ILE* 3.4 13.0 - - - +
26F ILE* 2.7 53.6 + - + +
125F ASP* 4.2 1.0 - - - -
126F LEU* 1.3 71.9 - - - +
128F PHE* 1.3 69.5 + - - +
129F PRO* 3.6 11.3 - - - +
130F GLU 4.8 1.0 + - - -
303F LYS* 4.2 1.3 - - - +
352F LEU* 4.0 23.3 - - + -
353F GLU 3.2 26.9 - - - -
354F GLN* 3.5 19.5 - - - +
355F LYS 5.3 0.9 - - - -
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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