Contacts of the strand formed by residues 121 - 128 (chain C) in PDB entry 1J7H
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 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 3.9 0.5 - - - +
35C PRO* 3.3 25.9 - - + +
47C ILE* 4.4 5.2 - - + +
50C GLN* 3.4 35.4 - - + +
51C ALA* 3.7 21.8 - - + +
54C SER* 3.3 30.1 - - - +
77C VAL* 4.9 7.0 - - + -
78C PHE 3.2 13.5 - - - +
79C VAL* 5.0 5.2 - - + -
88C VAL* 5.7 4.7 - - + -
115C LEU* 3.4 5.8 - - - +
119C VAL* 3.1 12.4 + - - +
120C GLY* 1.3 80.3 - - - +
122C GLU* 1.3 62.1 + - - +
123C ILE* 4.1 9.9 - - + -
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Residues in contact with GLU 122 (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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108B SER* 5.7 0.4 - - - -
109B CYS 3.5 9.8 + - - +
110B VAL* 3.1 27.7 - - - +
32C GLY* 2.5 33.8 - - - +
33C GLN 3.2 10.7 - - - +
34C ILE* 3.4 10.7 - - + +
77C VAL* 2.7 38.6 - - - +
78C PHE* 3.0 14.1 + - + -
115C LEU* 3.5 15.0 - - + +
116C PRO* 3.5 17.6 - - - +
121C LEU* 1.3 75.6 - - - +
123C ILE* 1.3 62.7 + - - +
124C GLU* 3.4 14.5 - - - +
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Residues in contact with ILE 123 (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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31C SER 2.8 4.5 - - - +
32C GLY* 3.1 0.9 - - - -
33C GLN* 2.6 35.8 + - + +
51C ALA 4.7 1.6 - - - +
54C SER* 2.9 50.7 - - - +
55C LEU* 3.7 20.4 - - + +
58C VAL* 3.4 27.8 - - + -
75C THR* 4.8 7.9 - - + -
76C THR 3.6 6.3 - - - +
77C VAL* 4.1 15.5 - - + -
92C TYR* 6.2 0.7 - - + -
121C LEU* 4.1 6.7 - - + -
122C GLU* 1.3 83.3 - - - +
124C GLU* 1.3 67.2 + - - +
125C ALA* 4.9 0.7 - - + +
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Residues in contact with GLU 124 (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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74B LYS* 5.6 5.6 - - - -
108B SER* 3.1 20.1 + - - +
30C THR* 3.6 18.4 - - - +
32C GLY* 3.5 17.5 - - - +
76C THR* 2.8 56.9 + - + +
78C PHE* 2.8 50.1 - - + -
122C GLU* 3.4 12.1 - - - +
123C ILE* 1.3 76.8 - - - +
125C ALA* 1.3 59.7 + - - +
126C ILE* 5.6 1.5 - - - +
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Residues in contact with ALA 125 (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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30C THR* 3.0 40.0 + - + +
58C VAL* 5.1 7.2 - - + -
62C ILE* 6.0 0.7 - - + -
72C ILE* 3.8 14.6 - - + -
74C LYS 3.0 18.2 - - - +
75C THR* 3.2 26.9 - - + +
123C ILE* 4.3 1.9 - - + +
124C GLU* 1.3 75.6 - - - +
126C ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 126 (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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74B LYS* 5.7 8.7 - - - +
27C LEU* 3.5 24.2 - - + -
28C VAL 2.9 22.7 - - - +
29C LEU* 3.7 33.4 - - + -
30C THR* 4.9 2.0 - - - +
72C ILE* 3.0 13.8 - - - +
73C VAL* 2.8 34.2 + - + -
74C LYS* 2.7 26.8 + - + +
124C GLU 5.6 0.9 - - - -
125C ALA* 1.3 83.1 - - - +
127C ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 127 (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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27C LEU* 3.3 4.9 - - - +
28C VAL* 2.6 61.1 + - + +
30C THR* 6.0 0.6 - - + +
62C ILE* 4.3 17.7 - - + -
67C LEU* 4.5 3.4 - - + -
68C THR 4.8 0.2 - - - +
71C ASP* 4.3 2.9 - - + -
72C ILE* 3.8 23.8 - - + +
73C VAL 3.9 0.9 - - - +
126C ILE* 1.3 76.0 - - - +
128C VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 128 (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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3A THR* 3.4 22.0 - - + -
24A LEU* 3.6 18.4 - - + -
26C ASN 3.2 9.0 - - - +
27C LEU* 3.1 25.8 - - + -
67C LEU* 2.8 24.7 - - - +
71C ASP* 3.1 24.6 + - - +
73C VAL* 3.0 35.7 - - + -
127C ALA* 1.3 72.9 - - - +
129C ARG* 1.3 62.9 + - - +
130C LYS* 4.7 4.7 - - + +
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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