Contacts of the strand formed by residues 122 - 129 (chain B) in PDB entry 2J2M
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 GLY 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR* 2.6 45.1 + - - +
120B GLU 3.6 1.0 - - - -
121B GLU* 1.3 78.8 - - - +
123B ASN* 1.3 66.1 + - - -
321B VAL* 3.5 2.1 - - - +
359B PRO* 5.1 0.7 - - - -
361B ALA* 3.8 3.8 - - - +
12D GLN 3.1 15.3 - - - -
13D GLY* 3.5 12.4 + - - -
14D VAL* 4.0 2.5 - - - -
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Residues in contact with ASN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 3.9 17.6 - - + +
117B PHE 3.2 6.1 - - - +
118B TYR* 3.5 30.3 - - - -
122B GLY* 1.3 74.9 - - - -
124B TRP* 1.3 59.1 + - - +
125B ASP* 4.9 0.7 - - - +
319B VAL* 3.3 21.9 - - + +
320B LEU 4.2 3.6 - - - +
321B VAL* 3.9 6.2 - - - +
357B ASN 3.1 26.3 + - - -
359B PRO* 3.3 28.1 - - - +
360B PHE 3.8 0.7 + - - -
12D GLN* 2.9 33.9 + - - +
14D VAL* 4.6 0.7 - - - +
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Residues in contact with TRP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 3.6 32.5 - + + -
81B LEU* 5.5 0.9 - - + -
116B LYS* 3.6 0.9 - - - -
117B PHE* 2.7 81.0 + + + -
119B THR* 5.1 1.8 + - - +
122B GLY 3.8 1.2 + - - -
123B ASN* 1.3 73.3 - - - +
125B ASP* 1.3 83.8 + - - +
126B PHE* 4.4 13.2 - + + -
201B PHE* 5.9 0.8 - - - -
203B TRP* 5.2 3.1 - + - -
215B LEU* 3.7 32.8 - - + -
217B TRP* 6.0 0.2 - + - -
260B LEU* 4.9 11.4 - - + -
319B VAL 3.3 13.2 - - - -
320B LEU* 3.4 25.5 - - + +
321B VAL* 4.1 19.3 - - + +
324B MET* 3.7 25.1 - - + -
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL 3.3 3.8 - - - +
116B LYS* 2.8 39.8 + - - +
123B ASN* 4.9 0.7 - - - +
124B TRP* 1.3 93.7 + - - +
126B PHE* 1.3 59.3 + - - +
127B VAL* 3.8 9.5 + - + -
314B GLY 4.1 0.3 - - - +
315B PHE* 3.2 11.0 - - + -
316B ASN 2.7 42.8 + - - +
317B PRO* 3.9 14.0 - - - +
319B VAL* 3.0 24.6 + - - +
12D GLN* 5.3 0.3 + - - +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.3 30.1 - + + -
114B SER* 3.2 3.1 - - - -
115B VAL* 2.7 47.0 + - + +
117B PHE* 4.3 14.3 - - + -
124B TRP* 4.0 13.1 + + + +
125B ASP* 1.3 71.9 - - - +
127B VAL* 1.3 61.9 + - - +
128B GLY* 3.5 10.1 - - - -
196B SER 3.6 26.2 - - - -
197B SER* 3.6 13.2 - - - -
201B PHE* 6.4 1.1 - + - -
215B LEU* 3.6 41.7 - - + -
217B TRP* 3.3 39.5 - + + +
315B PHE* 4.7 0.2 - - - -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE 3.9 2.0 - - - -
114B SER* 3.7 15.7 - - - +
125B ASP* 3.8 4.7 + - + -
126B PHE* 1.3 81.0 - - - +
128B GLY* 1.3 57.3 + - - +
197B SER* 4.8 3.4 - - - +
201B PHE* 5.9 0.5 - - - -
315B PHE* 3.4 29.6 - - + -
316B ASN 3.8 2.5 - - - +
317B PRO* 3.6 31.5 - - + +
335B ARG* 3.0 43.6 + - - +
339B TYR* 3.8 12.3 - - + -
501B HEM 3.8 19.9 - - + +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 2.7 40.3 + - - -
126B PHE* 3.5 8.4 - - - -
127B VAL* 1.3 75.1 - - - +
129B ASN* 1.3 55.4 + - - -
196B SER 3.2 16.8 - - - -
197B SER* 4.7 2.2 - - - -
501B HEM 3.2 23.1 - - - +
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS* 3.4 15.4 + - - -
97B VAL* 5.2 0.2 - - - +
110B PRO* 3.8 19.2 - - + +
111B ARG 3.1 7.5 - - - +
112B GLY* 3.3 21.5 + - - -
113B PHE* 4.2 2.2 - - - +
128B GLY* 1.3 73.3 - - - +
130B ASN* 1.3 60.7 + - - +
131B LEU* 3.4 15.5 - - + +
133B VAL 5.7 0.9 + - - +
134B PHE* 3.6 26.3 - - - -
176B MET* 5.2 0.6 - - - +
195B GLY* 4.3 2.5 - - - -
196B SER* 2.7 35.7 + - - +
198B VAL* 4.7 1.1 - - + +
501B HEM 3.5 28.8 - - + +
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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
------------------------------------------------------------
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