Contacts of the strand formed by residues 41 - 51 (chain F) in PDB entry 1XE0
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 GLU 41 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F ASN* 1.3 71.7 - - - +
42F HIS* 1.3 61.5 + - - +
43F GLN* 4.4 24.7 - - + +
118F LEU 3.8 0.3 - - - +
119F VAL* 3.3 4.9 - - - +
120F ALA* 2.8 53.4 + - + +
121F LEU 5.5 2.0 - - - -
122F GLU* 4.6 13.2 - - + +
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Residues in contact with HIS 42 (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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33F PHE* 5.4 1.1 - - + -
35F VAL* 3.3 26.9 - - + +
38F ASP 3.0 21.8 + - - -
40F ASN* 3.4 24.3 + - - +
41F GLU* 1.3 76.8 - - - +
43F GLN* 1.3 72.5 + - - +
97F THR* 4.7 1.7 - - - +
98F PRO* 3.3 31.5 - - + +
117F HIS* 2.9 27.4 - - + -
118F LEU 3.2 5.4 - - - +
119F VAL* 3.6 10.5 - - + +
69G TYR* 3.1 35.2 - + - -
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Residues in contact with GLN 43 (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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33F PHE* 4.6 6.1 - - - -
41F GLU* 4.4 21.6 - - + +
42F HIS* 1.3 82.0 + - - +
44F LEU* 1.3 63.2 + - - +
45F SER 3.8 0.5 + - - -
95F GLU* 3.5 25.7 - - + +
96F ILE 3.3 18.4 + - - -
97F THR* 3.1 22.9 + - - +
98F PRO* 4.6 0.4 - - - -
116F GLN 3.7 0.2 - - - +
117F HIS* 3.5 4.2 + - - -
118F LEU* 2.8 44.6 + - + +
17J ASN* 3.0 28.4 + - - +
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Residues in contact with LEU 44 (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 PHE* 3.5 44.4 - - + -
33F PHE* 3.9 34.5 - - + -
43F GLN* 1.3 72.1 - - - +
45F SER* 1.3 58.1 + - - +
46F LEU* 3.6 25.8 - - + -
94F PHE 3.3 2.8 - - - +
95F GLU* 3.2 2.0 - - - -
96F ILE* 2.7 43.7 + - + +
100F VAL* 3.9 22.9 - - + -
102F LEU* 4.3 14.4 - - + -
116F GLN 3.5 8.7 - - - +
117F HIS 5.2 0.2 - - - +
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Residues in contact with SER 45 (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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43F GLN 3.8 1.2 + - - -
44F LEU* 1.3 72.6 - - - +
46F LEU* 1.3 61.8 + - - +
47F ARG* 3.6 2.6 + - - +
93F GLY* 3.2 27.9 - - - -
94F PHE 3.5 3.8 - - - -
95F GLU* 3.6 18.0 + - - +
115F GLY* 3.1 4.0 - - - -
116F GLN* 2.8 61.7 + - - -
118F LEU* 4.0 8.9 - - - +
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Residues in contact with LEU 46 (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 PHE* 4.7 1.6 - - + -
44F LEU* 3.6 35.0 - - + -
45F SER* 1.3 73.4 + - - +
47F ARG* 1.3 60.7 + - - +
48F THR 5.3 0.4 - - - +
49F VAL* 6.0 0.2 - - + -
78F LEU* 4.0 25.1 - - + -
91F LEU* 3.6 26.6 - - + +
93F GLY 2.9 7.3 + - - -
94F PHE* 2.9 39.5 + - + +
96F ILE* 3.9 24.5 - - + -
102F LEU* 4.4 10.5 - - + -
113F VAL* 3.8 25.8 - - + -
114F SER 3.8 3.8 - - - +
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Residues in contact with ARG 47 (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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45F SER* 4.2 3.3 + - - +
46F LEU* 1.3 77.1 - - - +
48F THR* 1.3 66.7 + - + +
90F SER* 3.4 5.2 + - - -
91F LEU* 2.8 25.1 + - - -
92F GLY* 3.6 14.4 + - - -
93F GLY* 3.5 27.1 - - - +
114F SER 2.8 13.8 + - - +
115F GLY* 3.9 9.6 - - - -
116F GLN* 4.3 17.8 + - + +
91G LEU* 3.0 23.9 + - - -
92G GLY 3.3 19.4 + - - -
93G GLY 3.4 18.6 + - - -
94G PHE* 3.5 50.5 - - + +
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Residues in contact with THR 48 (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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47F ARG* 1.3 87.9 + - + +
49F VAL* 1.4 67.1 + - - +
50F SER* 4.3 1.6 + - - -
88F THR* 4.3 10.1 - - + -
89F VAL 3.4 8.3 - - - -
90F SER* 4.3 10.1 - - - +
91F LEU* 4.5 1.6 - - - +
112F TYR 4.6 0.2 - - - -
113F VAL* 3.3 4.7 - - - +
114F SER* 2.7 49.2 + - - +
77G ALA 3.6 3.5 + - - -
78G LEU* 2.6 31.4 + - - +
91G LEU* 3.3 27.1 - - + -
94G PHE* 5.2 0.7 - - + -
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Residues in contact with VAL 49 (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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46F LEU* 6.0 0.2 - - + -
48F THR* 1.4 76.9 - - - +
50F SER* 1.3 64.3 + - - +
62F VAL* 3.9 20.9 - - + -
78F LEU* 5.4 4.7 - - + -
79F ALA* 4.6 14.8 - - + -
81F LEU* 3.5 15.4 - - + +
88F THR* 3.3 3.7 - - - +
89F VAL 2.9 33.3 + - - +
91F LEU* 3.9 25.8 - - + -
111F VAL* 3.6 24.7 - - + -
112F TYR 3.2 5.8 - - - +
113F VAL* 4.5 16.2 - - + -
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Residues in contact with SER 50 (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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48F THR* 4.8 0.5 + - - -
49F VAL* 1.3 76.8 - - - +
51F LEU* 1.3 63.6 + - - +
81F LEU* 4.0 0.7 - - - -
87F PRO 3.3 5.8 - - - -
88F THR* 3.6 20.4 - - - -
111F VAL* 3.4 3.6 - - - +
112F TYR* 2.7 52.6 + - - +
77G ALA* 3.9 17.5 + - - +
78G LEU 5.0 1.3 - - - -
79G ALA* 4.4 3.2 - - - -
80G SER* 3.9 18.1 + - - -
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Residues in contact with LEU 51 (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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50F SER* 1.3 74.6 - - - +
52F GLY* 1.3 68.7 + - - +
55F ALA* 4.3 5.2 - - + -
60F HIS* 3.6 24.9 - - + +
81F LEU* 3.7 14.6 - - + -
82F LYS* 3.6 17.5 - - - +
83F PRO* 3.4 44.4 - - + -
87F PRO* 2.9 23.0 + - + +
110F PRO 3.8 2.2 - - - +
111F VAL* 3.6 28.0 - - + -
112F TYR* 4.6 1.1 - - - -
59G LEU* 3.8 4.1 - - + +
80G SER* 2.7 27.8 + - - -
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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