Contacts of the strand formed by residues 10 - 18 (chain B) in PDB entry 5JTM
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 1.3 95.0 + - - +
11B PHE* 1.3 62.5 + - - +
12B GLN* 5.3 2.9 - - + +
85B SER* 3.6 13.0 - - - +
86B ILE* 3.1 22.0 - - - -
87B ALA* 3.0 26.5 + - + +
88B GLY* 5.5 0.3 - - - -
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.7 10.7 - - + -
10B THR* 1.3 76.0 - - - +
12B GLN* 1.3 75.1 + - - +
13B ILE* 4.1 3.8 - - + -
84B PHE* 3.6 28.3 - + + -
85B SER 3.3 3.4 - - - -
86B ILE* 3.6 18.6 - - + -
97B CYS* 3.9 15.5 - - - -
101B TYR* 3.9 16.2 - + - -
102B CYS* 3.5 25.1 - - - -
105B ILE* 3.6 27.8 - - + -
129D ALA* 5.5 0.2 - - - +
130D PRO* 3.8 30.0 - - + +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 5.7 3.4 - - + -
11B PHE* 1.3 88.3 + - - +
13B ILE* 1.3 70.1 + - - +
14B GLN* 3.7 18.2 + - - +
84B PHE* 3.4 6.2 - - - +
85B SER* 3.0 37.6 + - - -
129D ALA* 3.5 27.8 - - - +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.1 8.5 - - + -
12B GLN* 1.3 80.2 - - - +
14B GLN* 1.3 66.3 + - - +
15B ARG 4.0 5.8 - - - +
16B ILE* 3.6 29.4 - - + -
83B ILE 4.0 3.6 - - - +
84B PHE* 3.7 20.2 - - + -
105B ILE* 3.8 32.8 - - + -
111D ARG* 4.1 9.4 - - - +
127D ASN* 3.8 27.3 - - + +
128D LEU 3.9 20.9 - - - +
129D ALA* 5.2 2.3 - - - +
130D PRO* 4.2 7.3 - - + +
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLN* 3.7 24.3 - - - +
13B ILE* 1.3 73.4 - - - +
15B ARG* 1.4 66.0 + - + +
55B VAL* 5.0 5.6 - - + +
83B ILE* 2.9 41.6 + - + +
85B SER* 3.0 34.3 + - - +
127D ASN* 5.3 1.6 + - - -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.6 47.6 + - - +
122A THR* 2.9 49.8 + - + +
124A PRO* 6.0 0.4 - - - +
13B ILE* 3.7 2.6 - - - +
14B GLN* 1.4 82.8 - - + +
16B ILE* 1.3 65.0 + - - +
17B TYR* 3.5 15.9 - - + -
82B GLY* 3.4 2.1 - - - -
83B ILE* 2.9 35.2 + - + +
125D GLN* 3.9 11.8 - - + +
127D ASN* 4.4 4.3 - - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A THR* 4.2 1.9 - - - -
13B ILE* 3.6 27.1 - - + -
15B ARG* 1.3 74.0 - - - +
17B TYR* 1.3 67.3 + - - +
80B GLN* 3.3 17.3 - - - +
81B GLY 3.6 3.6 - - - +
82B GLY* 4.4 2.0 - - - -
84B PHE* 4.7 1.1 - - + -
105B ILE* 3.7 27.4 - - + -
106B LEU* 3.5 26.9 - - + -
109B TYR* 3.8 28.9 - - + +
125D GLN* 2.8 33.2 + - - +
127D ASN* 3.4 23.9 - - - +
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.5 28.9 - - + -
29A PRO* 3.4 15.4 - - - +
32A PHE* 3.9 19.1 - + - -
120A ARG 3.7 6.1 - - - -
121A GLY 4.0 6.7 - - - +
122A THR* 3.5 20.9 - - + -
15B ARG* 3.5 28.9 - - + -
16B ILE* 1.3 81.6 - - - +
18B THR* 1.3 65.0 + - - +
19B LYS* 3.4 21.0 + - + -
57B GLU* 3.3 31.8 - - - +
80B GLN* 3.3 8.0 - - - +
81B GLY 2.9 36.0 + - - +
83B ILE* 3.4 16.7 - - + +
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.1 23.9 - - + -
25A ALA* 4.6 1.9 - - - +
117A MET 5.1 0.7 - - - +
120A ARG* 3.0 36.3 + - + +
121A GLY* 3.3 8.8 - - - -
17B TYR* 1.3 72.3 - - - +
19B LYS* 1.3 60.0 + - - +
20B ASP 3.7 7.6 - - - +
21B ILE* 3.5 39.9 - - + -
78B VAL* 4.4 4.7 - - + -
79B GLN 3.7 4.3 - - - -
80B GLN* 3.1 19.6 + - - +
113B CYS* 4.1 7.3 - - - -
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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