Contacts of the strand formed by residues 109 - 115 (chain C) in PDB entry 5XAC
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 LEU 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C ILE* 4.2 6.7 - - + -
32C PRO 3.1 16.2 + - - +
33C VAL* 3.3 9.0 - - + +
34C ILE 2.8 26.3 + - - -
83C VAL* 3.8 19.7 - - + -
95C ILE* 3.8 16.6 - - + -
98C VAL* 4.0 13.2 - - + +
99C TYR* 3.9 23.6 - - + +
102C GLU* 3.8 32.3 - - + +
103C LYS* 4.1 2.0 - - - +
107C GLY 4.1 0.2 + - - -
108C PHE* 1.3 72.1 - - - +
110C TYR* 1.3 62.1 + - - +
111C MET* 3.6 29.6 - - + -
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.5 13.0 - + + -
8C LYS* 3.4 45.2 - - + +
16C ARG* 3.5 8.7 - - - -
34C ILE* 3.5 31.6 - - + -
36C GLU* 4.6 7.2 - - - -
83C VAL* 3.6 5.4 - - - +
84C ASN* 2.7 46.8 + - - +
102C GLU 5.3 0.2 + - - -
104C ASP* 3.6 17.9 - - + -
106C ASP* 2.6 29.1 + - - -
108C PHE* 3.5 22.1 - - + -
109C LEU* 1.3 74.2 - - - +
111C MET* 1.3 64.2 + - - +
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Residues in contact with MET 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.9 18.4 - - + -
34C ILE 2.8 12.9 + - - +
35C ILE* 4.3 6.1 - - + -
36C GLU* 3.1 24.0 + - - +
60C MET* 3.9 16.4 - - + -
63C LEU* 4.0 5.2 - - + -
81C LEU* 3.8 38.4 - - + -
82C LEU 3.3 9.0 - - - +
83C VAL* 4.3 16.4 - - + -
84C ASN 4.4 0.7 - - - +
85C GLY 5.2 0.4 - - - -
95C ILE* 3.5 31.4 - - + -
98C VAL* 4.8 0.4 - - + -
109C LEU* 3.6 17.5 - - + -
110C TYR* 1.3 80.0 - - - +
112C VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU* 3.0 21.1 - - + +
37C ARG 4.7 1.8 - - - +
38C TYR* 4.1 32.8 - - + +
39C LYS* 6.1 3.4 - - + -
80C PHE 3.7 0.5 - - - +
81C LEU* 3.4 5.9 - - - +
82C LEU* 2.7 50.9 + - + +
85C GLY* 3.5 33.9 - - - +
111C MET* 1.3 80.2 - - - +
113C TYR* 1.3 59.5 + - - +
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.9 20.2 - - + -
36C GLU* 3.0 24.0 + - - -
37C ARG* 3.5 37.9 + - + +
38C TYR* 3.0 22.7 + - - +
44C LEU* 4.0 18.6 - - + -
45C PRO 2.7 29.0 + - - -
46C VAL* 3.4 4.9 - - - +
47C LEU* 3.3 31.4 + - + +
67C ILE* 4.7 4.5 - - + -
71C LEU* 3.7 18.2 - - + -
79C PHE* 3.4 26.7 - + + -
80C PHE 3.1 4.7 - - - +
81C LEU* 4.2 5.2 - - + -
112C VAL* 1.3 74.8 - - - +
114C ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TYR* 3.5 30.1 - - + -
41C GLU* 3.6 9.2 - - - +
44C LEU* 3.6 10.6 - - - +
79C PHE 3.9 0.5 - - - -
80C PHE* 2.9 37.9 + - + +
82C LEU* 5.2 8.3 - - + -
112C VAL 5.5 0.2 - - - -
113C TYR* 1.3 78.7 - - - +
115C SER* 1.3 68.1 + - - +
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 2.8 39.5 + - - +
43C GLN* 4.1 15.7 - - - +
44C LEU* 3.5 8.4 - - - +
78C ALA* 3.7 11.4 - - - -
80C PHE* 4.6 2.7 - - - -
114C ALA* 1.3 78.1 - - - +
116C GLN* 1.3 67.1 + - - +
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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