Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 2J0M
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 TRP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS 5.7 0.3 - - - +
40A PHE* 5.4 3.6 - - - -
87A LEU* 3.5 40.4 - - + -
88A SER* 3.4 5.8 - - - -
89A HIS* 3.2 48.7 - + + -
90A LEU* 4.8 5.5 - - - +
96A HIS* 4.8 11.4 - + - -
111A PHE* 3.8 29.4 - + + -
112A GLU* 3.4 35.8 + - + +
115A HIS* 3.7 37.5 + + - -
117A PRO 3.6 14.1 + - - +
118A GLU 5.3 0.9 - - - -
119A GLU* 1.3 82.6 + - - +
121A LYS* 1.3 59.4 - - - +
122A TYR* 4.0 15.4 + + + -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.9 44.7 - - + -
42A TYR* 5.7 0.7 - - - -
50A THR* 5.0 2.6 + - - +
86A ARG 3.3 5.9 - - - +
87A LEU* 3.4 1.6 - - - -
88A SER* 2.9 42.0 + - - +
90A LEU* 4.9 17.2 - - + +
119A GLU 4.4 0.2 + - - -
120A TRP* 1.3 71.4 - - - +
122A TYR* 1.3 64.9 + - - +
123A GLU* 3.3 33.6 + - - +
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.4 47.7 - - + +
38A LYS 3.4 20.0 + - - +
39A VAL* 4.1 13.0 - - + -
40A PHE* 2.7 38.4 + - - +
85A LEU* 4.8 10.3 - - + -
86A ARG 3.5 2.5 - - - -
87A LEU* 3.5 45.6 - - + +
98A LEU* 4.4 13.2 - - + -
107A VAL* 4.9 3.8 - - + -
108A ARG* 4.1 15.6 + - - -
112A GLU* 4.0 18.3 + - - +
117A PRO 6.1 0.4 - - - -
120A TRP* 4.0 15.3 + - + +
121A LYS* 1.3 71.2 - - - +
123A GLU* 1.3 54.3 + - - +
124A LEU 4.3 0.2 - - - -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.2 14.8 - - + +
42A TYR* 2.5 34.4 + - + -
85A LEU* 3.7 4.3 - - - +
86A ARG* 2.7 74.2 + - + +
121A LYS* 3.3 33.1 - - - +
122A TYR* 1.3 75.2 - - - +
124A LEU* 1.3 72.4 + - - +
125A ARG* 3.2 17.6 + - + +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.4 6.6 - - + +
40A PHE 2.9 14.6 + - - +
41A HIS* 4.3 6.2 - - + -
42A TYR* 3.9 8.0 - - - -
43A PHE* 3.9 17.3 - - + -
68A ILE* 4.2 23.1 - - + -
71A ILE* 3.8 33.4 - - + -
72A VAL* 4.7 4.3 - - + -
83A TYR* 3.9 28.9 - - + -
84A GLY 3.5 17.0 - - - +
85A LEU* 4.0 12.5 - - + +
122A TYR 4.3 0.2 - - - -
123A GLU* 1.3 72.9 - - - +
125A ARG* 1.3 68.1 + - - +
146A PHE* 3.5 23.7 - - + -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.7 14.2 + - + -
83A TYR* 3.4 5.4 - - - +
84A GLY* 2.8 37.9 + - - +
86A ARG* 3.1 60.4 - - - +
97A TRP* 3.7 23.2 - - + -
123A GLU* 3.2 22.9 + - + +
124A LEU* 1.3 82.0 - - - +
126A ILE* 1.3 64.4 + - - +
127A ARG* 3.6 0.9 + - - +
146A PHE* 4.0 4.3 - - - -
150A GLN* 3.5 27.1 - - - +
153A ASN* 5.5 0.2 - - - +
154A ASP* 3.2 33.3 + - - -
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A CYS* 3.3 13.9 - - + +
83A TYR* 3.5 23.8 - - + +
97A TRP* 5.2 0.2 - - - -
125A ARG* 1.3 73.7 + - - +
127A ARG* 1.3 63.5 + - - +
128A TYR 4.6 1.1 - - - +
129A LEU* 4.0 19.3 - - + -
137A PHE* 4.2 7.2 - - + -
143A THR* 3.6 27.8 - - + +
146A PHE* 3.6 22.7 - - + -
147A PHE* 3.6 41.0 - - + +
150A GLN* 2.6 32.2 + - - +
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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