Contacts of the strand formed by residues 111 - 120 (chain J) 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 VAL 111 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J CYS 4.0 0.2 - - - +
23J GLU* 3.4 3.6 - - - +
24J LEU* 2.8 42.2 + - + +
49J VAL* 3.6 29.4 - - + -
50J SER 3.5 7.0 - - - +
51J LEU* 3.4 24.2 - - + -
60J HIS* 3.8 12.1 - - + +
62J VAL* 3.6 15.5 - - + -
81J LEU* 4.8 0.4 - - + -
104J LEU* 3.5 29.4 - - + -
109J GLY* 4.0 1.8 - - - -
110J PRO* 1.3 75.8 - - - +
112J TYR* 1.3 68.2 + - - +
113J VAL* 5.1 1.8 - - + -
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Residues in contact with TYR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F VAL* 6.6 0.4 - - + -
75F LYS 6.0 1.1 - - - -
76F ILE* 5.8 0.9 - - - -
77F ALA* 3.6 39.0 - - + +
105F LYS* 4.4 18.3 + - - -
22J CYS 3.5 6.1 - - - -
23J GLU* 2.8 44.1 + - + -
49J VAL* 3.1 8.0 - - - +
50J SER* 2.9 42.8 + - - +
51J LEU 4.9 0.2 - - - -
52J GLY* 4.0 15.7 - - - -
110J PRO* 3.4 27.5 - - + +
111J VAL* 1.3 75.1 - - - +
113J VAL* 1.3 67.2 + - - +
114J SER 4.2 0.2 - - - -
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Residues in contact with VAL 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ILE* 5.2 0.9 - - - +
77F ALA 5.0 0.9 + - - -
20J PHE* 4.3 4.3 - - + -
21J GLY* 3.1 5.3 - - - -
22J CYS* 3.0 47.0 + - - +
24J LEU* 4.3 18.6 - - + -
46J LEU* 3.8 31.9 - - + -
48J THR 3.4 8.1 - - - +
49J VAL* 4.3 19.3 - - + -
62J VAL* 4.7 7.4 - - + -
78J LEU* 6.2 0.9 - - + -
102J LEU* 4.0 13.2 - - + -
111J VAL* 5.1 0.9 - - + -
112J TYR* 1.3 81.6 - - - +
114J SER* 1.3 64.1 - - - +
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Residues in contact with SER 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ILE* 4.0 20.0 - - - -
77F ALA 3.4 23.0 + - - -
78F LEU* 4.2 1.5 - - - -
94F PHE* 3.4 15.9 - - - -
20J PHE* 3.5 6.1 - - - -
46J LEU* 3.7 3.3 - - - -
47J ARG 2.7 27.6 + - - -
48J THR* 2.7 35.0 + - - +
113J VAL* 1.3 78.6 - - - +
115J GLY* 1.3 53.6 + - - +
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Residues in contact with GLY 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ILE* 4.5 0.2 - - - +
94F PHE* 3.5 20.6 - - - -
19J LEU* 3.8 2.9 - - - -
20J PHE* 2.9 35.6 + - - +
45J SER 3.3 13.0 - - - -
46J LEU* 4.4 0.4 - - - -
47J ARG* 3.9 4.5 - - - -
114J SER* 1.3 76.1 - - - +
116J GLN* 1.3 64.4 + - - -
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Residues in contact with GLN 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 3.9 16.7 - - + -
95F GLU* 3.0 38.0 + - - +
17J ASN* 3.6 22.3 - - - +
18J PHE 3.3 5.4 - - - +
19J LEU* 6.0 0.2 - - - -
20J PHE* 4.0 4.5 - - - +
43J GLN 3.8 0.3 - - - +
44J LEU* 3.7 4.2 - - - +
45J SER* 2.8 51.8 + - - +
47J ARG* 4.5 15.1 + - + +
115J GLY* 1.3 78.0 - - - +
117J HIS* 1.4 59.3 + - - +
118J LEU* 3.7 23.2 + - + +
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Residues in contact with HIS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F TYR* 3.4 39.3 - + + -
17J ASN* 3.7 0.5 - - - -
18J PHE* 2.8 48.8 + - + +
19J LEU 5.0 1.6 - - - +
20J PHE* 4.0 12.8 - + + +
33J PHE* 3.7 33.3 - + + -
35J VAL* 5.1 3.0 - - - +
42J HIS* 2.7 43.9 + + + -
43J GLN 3.7 5.9 + - - -
44J LEU* 4.8 2.0 - - + -
116J GLN* 1.4 71.0 - - - +
118J LEU* 1.3 65.9 + - - +
119J VAL* 3.7 10.1 - - + +
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Residues in contact with LEU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J SER* 5.0 11.4 - - - +
16J GLN 3.2 12.6 - - - +
17J ASN* 3.9 20.2 - - + +
41J GLU 4.4 0.7 - - - -
42J HIS* 3.3 5.4 - - - -
43J GLN* 2.9 48.1 + - + +
45J SER* 4.0 16.8 - - - -
95J GLU* 4.0 21.1 - - - +
116J GLN* 3.7 27.1 - - + +
117J HIS* 1.3 74.2 + - - +
119J VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F TYR* 4.0 17.5 - - + -
15J SER* 3.4 3.1 - - - -
16J GLN* 2.6 59.3 + - + +
18J PHE* 4.0 11.4 - - + -
39J GLU 5.2 0.2 - - - +
40J ASN* 3.8 31.4 - - + +
41J GLU 3.3 4.3 - - - -
42J HIS* 3.8 13.5 - - + +
117J HIS* 3.7 22.4 - - + +
118J LEU* 1.3 80.3 - - - +
120J ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J SER* 3.7 21.7 - - - +
16J GLN* 5.6 0.9 - - - -
40J ASN* 3.4 21.4 + - - +
41J GLU* 2.9 44.6 + - + +
119J VAL* 1.3 74.2 - - - +
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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