Contacts of the strand formed by residues 118 - 127 (chain B) in PDB entry 3JRQ
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 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B A8S 4.5 2.8 - - - +
108B VAL 3.1 10.1 - - - +
109B ASN* 3.3 22.9 - - - +
110B VAL* 4.6 2.4 - - - +
116B ALA 4.0 0.4 - - - -
117B ASN* 1.3 84.7 - - + +
119B SER* 1.3 61.8 + - - +
120B ARG* 4.6 7.5 + - - +
140B GLY* 3.5 5.7 - - - -
141B GLU* 3.1 34.2 + - - +
142B HIS* 3.2 20.8 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A8S 4.0 14.8 - - - -
106B ARG 3.9 0.5 - - - +
107B ASP* 3.5 2.1 - - - +
108B VAL* 2.7 48.8 + - - +
118B THR* 1.3 77.3 - - - +
120B ARG* 1.3 65.2 + - - +
121B GLU* 3.0 29.0 + - - +
137B ILE* 3.6 19.9 - - - +
139B GLY 3.6 6.7 - - - -
140B GLY* 4.3 0.4 - - - -
142B HIS* 3.8 1.8 + - - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 5.7 2.7 - - - +
106B ARG 3.2 6.1 - - - -
107B ASP* 3.7 27.8 - - + +
118B THR* 4.6 8.1 + - - +
119B SER* 1.3 79.1 - - - +
121B GLU* 1.3 58.3 + - - +
137B ILE* 3.4 8.1 - - - +
138B THR* 2.9 42.8 + - - +
139B GLY* 3.1 14.2 + - - +
140B GLY* 3.5 30.0 - - - +
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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
----------------------------------------------------------
1B A8S 4.6 11.3 + - - +
79B PHE* 3.7 3.8 - - + -
86B LYS* 4.8 0.2 + - - -
105B THR* 3.3 7.6 + - - -
106B ARG* 2.5 82.1 + - + +
108B VAL* 4.1 12.2 - - - +
119B SER* 3.0 26.3 + - - +
120B ARG* 1.3 81.5 - - - +
122B ARG* 1.3 61.3 + - - +
135B PHE* 4.0 18.3 - - + -
136B SER 3.2 9.0 - - - +
137B ILE* 4.0 15.5 - - + +
138B THR* 4.2 2.2 + - - -
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.7 3.4 - - - -
102B VAL* 5.5 3.4 - - - +
103B GLY* 3.7 24.8 - - - +
104B CYS 3.3 12.1 - - - +
105B THR* 4.4 7.2 - - - +
121B GLU* 1.3 75.2 - - - +
123B LEU* 1.3 67.4 + - - +
124B ASP* 2.7 33.3 + - - +
135B PHE* 3.0 4.3 - - - -
136B SER* 2.8 51.5 + - - +
138B THR* 3.9 23.0 - - + +
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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
----------------------------------------------------------
79B PHE* 3.4 30.3 - - + -
100B MET* 4.3 13.5 - - + -
101B ARG* 3.6 23.3 - - - +
102B VAL* 3.8 4.1 - - - +
103B GLY* 2.8 27.9 + - - -
104B CYS* 3.0 39.3 + - - +
122B ARG* 1.3 73.8 + - - +
124B ASP* 1.3 59.6 + - - +
125B LEU 3.2 26.2 - - - +
126B LEU* 4.1 16.8 - - + -
133B THR* 3.4 15.0 - - - +
134B GLY 3.6 7.0 - - - +
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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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102B VAL* 3.6 18.9 - - - +
122B ARG* 2.7 44.7 + - - +
123B LEU* 1.3 75.4 - - - +
125B LEU* 1.3 66.3 + - + +
134B GLY 2.8 15.0 + - - +
135B PHE 3.3 13.2 - - - -
136B SER* 2.6 23.9 + - - -
148B LYS* 3.5 23.6 + - - +
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Residues in contact with LEU 125 (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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47B PHE* 5.0 9.0 - - + -
102B VAL* 3.9 5.8 - - - +
123B LEU* 3.2 8.5 - - - +
124B ASP* 1.3 85.4 - - + +
126B LEU* 1.3 62.3 + - - +
127B ASP* 5.0 9.6 - - + +
132B VAL* 3.3 37.0 - - + +
133B THR* 3.0 26.1 + - - +
134B GLY* 3.1 11.0 + - - +
148B LYS* 5.7 1.8 - - - +
150B VAL* 4.5 15.0 - - + -
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Residues in contact with LEU 126 (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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73B TRP* 4.3 6.7 - - + -
77B ARG* 3.8 48.2 - - + +
79B PHE* 5.8 0.2 - - + -
100B MET* 4.0 26.2 - - + +
101B ARG* 5.8 2.2 - - - -
102B VAL* 4.2 11.8 - - + +
123B LEU* 4.1 20.6 - - + -
125B LEU* 1.3 74.5 - - - +
127B ASP* 1.3 61.4 + - - +
128B ASP* 4.0 6.4 + - - +
132B VAL 3.4 2.9 - - - -
133B THR* 3.3 25.6 - - - +
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Residues in contact with ASP 127 (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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47B PHE* 5.9 0.2 - - - -
73B TRP* 3.6 2.5 - - - -
125B LEU* 5.0 7.9 - - + -
126B LEU* 1.3 75.8 - - - +
128B ASP* 1.3 56.5 + - - +
129B ASP* 3.1 22.9 + - - +
130B ARG* 3.3 33.5 + - - +
131B ARG* 2.8 26.2 + - - -
132B VAL* 2.8 31.6 + - + +
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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