Contacts of the strand formed by residues 10 - 18 (chain D) in PDB entry 5JTO
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 THR 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLU* 3.4 13.7 + - - +
9D MET* 1.3 80.8 + - - +
11D PHE* 1.3 66.7 + - - +
12D GLN* 3.8 26.0 - - + +
54D ASP* 6.6 0.2 - - + -
85D SER* 3.1 15.2 - - - +
86D ILE* 3.8 1.6 - - - +
87D ALA* 3.0 46.7 + - + +
89D ILE* 5.4 1.7 - - - +
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Residues in contact with PHE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D MET* 4.6 17.5 - - + +
10D THR* 1.3 78.9 - - - +
12D GLN* 1.3 68.2 - - - +
13D ILE* 4.6 11.4 - - + -
84D PHE* 3.7 35.0 - + + -
85D SER 3.1 5.6 - - - -
86D ILE* 4.3 19.3 - - + -
89D ILE* 5.2 5.4 - - + -
97D CYS* 4.7 9.0 - - - -
101D TYR* 3.5 38.4 - + - -
102D CYS* 3.8 29.4 - - - -
105D ILE* 4.8 6.1 - - + -
309F THR* 5.1 5.0 - - - +
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Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 3.8 20.3 - - + +
11D PHE* 1.3 82.8 - - - +
13D ILE* 1.3 64.8 + - - +
14D GLN* 3.5 1.5 + - + -
84D PHE* 4.7 1.3 - - - -
85D SER* 2.9 45.0 + - - +
307F THR 3.1 26.5 + - - +
308F CYS* 3.4 19.2 - - - +
309F THR* 4.0 20.8 + - - +
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Residues in contact with ILE 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO* 4.0 27.5 - - + +
11D PHE* 4.6 9.0 - - + -
12D GLN* 1.3 70.9 - - - +
14D GLN* 1.3 61.7 + - - +
15D ARG 3.6 14.1 - - - +
16D ILE* 3.6 25.8 - - + -
83D ILE 3.6 7.2 - - - +
84D PHE* 3.8 19.5 - - + -
105D ILE* 3.4 37.2 - - + -
306F VAL* 3.4 18.8 - - - +
308F CYS 5.1 0.2 - - - -
309F THR* 2.9 39.2 + - + +
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Residues in contact with GLN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 4.7 7.1 - - + -
12D GLN* 3.5 2.2 + - + +
13D ILE* 1.3 73.9 - - - +
15D ARG* 1.3 63.6 + - + +
55D VAL* 3.4 26.7 - - - +
83D ILE* 3.0 33.4 + - + +
85D SER* 2.9 27.1 + - - +
304F PRO* 3.1 34.8 - - + +
305F ALA* 3.2 3.8 - - - +
306F VAL* 3.0 43.1 + - - +
307F THR* 5.6 1.1 - - - +
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Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO* 6.0 0.2 - - - -
28C ALA 2.8 30.3 + - - -
29C PRO 4.5 0.2 - - - -
31C VAL* 3.9 1.4 - - - +
32C PHE* 3.4 32.7 - - + -
121C GLY 2.8 26.5 + - - -
122C THR* 2.8 19.4 + - + +
123C PHE* 3.4 24.9 - - - -
13D ILE* 3.5 3.9 - - - +
14D GLN* 1.3 83.0 - - + +
16D ILE* 1.3 71.1 + - - +
17D TYR* 3.6 29.8 + - + -
82D GLY* 3.5 2.6 - - - -
83D ILE* 2.9 41.6 + - + +
301F ILE* 4.1 15.8 - - + +
305F ALA* 4.6 7.0 - - + -
306F VAL* 5.2 3.4 - - - -
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Residues in contact with ILE 16 (chain D).
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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111B ARG* 3.4 39.2 + - - +
129B ALA* 5.5 0.2 - - - -
130B PRO* 3.5 28.9 - - + -
122C THR* 3.1 22.7 - - + +
13D ILE* 3.6 24.0 - - + -
15D ARG* 1.3 78.6 - - - +
17D TYR* 1.3 61.0 + - - +
80D GLN* 4.0 7.4 - - - +
81D GLY 3.9 5.8 - - - +
82D GLY* 4.9 0.4 - - - -
84D PHE* 5.5 0.4 - - + -
105D ILE* 5.2 1.3 - - + -
106D LEU* 4.6 16.6 - - + -
109D TYR* 4.1 26.7 - - + -
306F VAL* 6.0 1.1 - - + -
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Residues in contact with TYR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 5.5 1.1 - - + -
28C ALA* 3.4 33.2 - - + +
29C PRO* 3.7 9.4 - - - +
120C ARG 3.2 15.9 - - - +
121C GLY* 3.9 4.9 - - - -
122C THR* 3.7 12.1 - - - +
15D ARG* 3.6 42.2 - - + -
16D ILE* 1.3 79.0 - - - +
18D THR* 1.3 72.4 + - - +
19D LYS* 3.5 15.4 - - + -
57D GLU* 2.9 24.2 + - - -
80D GLN* 3.3 15.5 + - - +
81D GLY* 2.8 44.1 + - - +
83D ILE* 3.9 19.7 - - + +
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Residues in contact with THR 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 3.2 22.0 - - - -
25C ALA* 4.5 0.2 - - - +
120C ARG* 3.0 35.6 + - + +
121C GLY* 3.4 7.4 + - - -
17D TYR* 1.3 75.4 - - - +
19D LYS* 1.3 59.5 + - - +
21D ILE* 3.4 22.3 - - + +
78D VAL* 3.8 5.4 - - + -
79D GLN 3.7 5.6 - - - -
80D GLN* 3.4 23.1 - - - +
113D CYS* 3.6 27.6 - - + -
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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