Contacts of the strand formed by residues 115 - 124 (chain B) in PDB entry 4JDA
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU* 3.2 27.8 + - - +
105B VAL 2.9 18.2 + - - -
106B SER* 4.9 1.8 - - - -
107B VAL* 3.8 5.8 - - - +
114B SER* 1.3 87.2 + - - +
116B SER* 1.3 60.9 + - - +
117B VAL* 5.2 0.8 - - + +
137B GLY* 3.8 6.5 - - - -
138B GLU* 3.4 27.8 + - + +
139B HIS* 3.3 20.8 + - - +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG 3.9 0.3 - - - +
104B GLU* 3.3 3.5 - - - +
105B VAL* 2.7 50.4 + - - +
107B VAL* 5.5 2.9 - - - -
115B THR* 1.3 78.5 + - - +
117B VAL* 1.3 63.7 + - - +
118B GLU* 4.2 3.3 + - - +
132B PHE* 5.9 0.2 - - - -
134B VAL* 3.8 17.5 - - - +
136B GLY 3.9 4.9 - - - -
137B GLY* 4.5 0.2 - - - -
139B HIS* 3.8 7.0 - - - -
301B A9S 3.3 31.5 - - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 5.5 5.8 - - + -
103B ARG 3.4 9.4 - - - +
104B GLU* 4.5 19.1 - - + +
115B THR* 5.2 0.2 - - - +
116B SER* 1.3 74.7 - - - +
118B GLU* 1.3 58.6 + - - +
134B VAL* 3.4 4.5 - - - +
135B LEU* 2.7 56.3 + - + -
136B GLY* 3.1 27.0 + - - +
137B GLY* 3.7 6.7 - - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.4 7.7 - - - -
102B ILE* 3.5 2.1 - - - -
103B ARG* 3.0 52.3 + - + +
105B VAL* 5.9 0.2 - - + -
116B SER* 5.1 4.3 - - - +
117B VAL* 1.3 77.2 - - - +
119B ILE* 1.3 59.6 + - - +
132B PHE* 3.4 32.8 - - + -
133B ARG 3.2 6.5 - - - +
134B VAL* 4.5 4.0 - - + -
135B LEU* 4.8 2.5 - - - -
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Residues in contact with ILE 119 (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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72B PHE* 4.0 2.5 - - - -
100B GLY* 3.0 32.8 - - - +
101B THR 3.4 7.6 - - - +
102B ILE* 3.9 11.7 - - + -
118B GLU* 1.3 72.4 - - - +
120B LEU* 1.3 70.8 + - - +
121B GLU* 3.7 24.7 - - + +
132B PHE* 3.3 4.5 - - - +
133B ARG* 2.9 37.2 + - + +
135B LEU* 3.6 28.2 - - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.7 25.4 - - + -
97B ILE* 3.5 32.1 - - + -
98B LYS 3.6 17.9 - - - +
99B VAL* 3.7 6.7 - - - +
100B GLY* 2.9 24.2 + - - -
101B THR* 2.8 17.1 + - - +
119B ILE* 1.3 75.5 - - - +
121B GLU* 1.3 62.4 + - - +
122B VAL 3.9 9.0 - - - +
123B LEU* 4.0 18.2 - - + -
130B LEU* 3.8 27.6 - - + -
131B SER 3.4 19.3 - - - +
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Residues in contact with GLU 121 (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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99B VAL* 3.4 23.8 - - - +
119B ILE* 3.7 20.8 - - + +
120B LEU* 1.3 80.9 - - - +
122B VAL* 1.3 72.5 + - + +
131B SER* 2.9 20.1 + - - +
132B PHE 4.8 0.7 - - - -
133B ARG* 3.5 28.5 + - + +
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Residues in contact with VAL 122 (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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40B HIS* 5.9 4.0 - - + +
99B VAL* 4.2 1.3 - - - -
120B LEU* 3.9 4.6 - - - +
121B GLU* 1.3 86.9 - - + +
123B LEU* 1.3 62.3 + - - +
124B ASP* 4.3 13.0 - - + +
129B ILE* 4.0 22.0 - - + +
130B LEU* 3.1 8.1 - - - -
131B SER* 2.9 48.3 + - - +
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Residues in contact with LEU 123 (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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66B TRP* 3.6 31.6 - - + -
70B ARG* 4.3 15.9 - - + +
97B ILE* 3.4 41.7 - - + +
98B LYS* 4.8 2.5 - - - -
99B VAL* 3.9 17.3 - - + +
120B LEU* 4.0 13.9 - - + -
122B VAL* 1.3 74.2 - - - +
124B ASP* 1.3 59.5 + - - +
125B GLU* 3.8 21.7 + - + +
129B ILE 3.8 0.4 - - - -
130B LEU* 4.5 13.5 - - + -
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Residues in contact with ASP 124 (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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40B HIS* 5.3 4.3 - - - -
66B TRP* 4.2 1.8 - - - -
122B VAL* 4.3 10.8 - - + +
123B LEU* 1.3 72.9 - - - +
125B GLU* 1.3 52.7 + - - +
126B GLU* 3.2 6.1 + - - +
127B LYS* 2.6 53.1 + - - +
128B ARG* 2.6 38.3 + - - -
129B ILE* 3.1 25.5 + - + +
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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