Contacts of the strand formed by residues 122 - 129 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLN 3.1 13.9 - - - -
13A GLY* 3.5 12.3 + - - -
14A VAL* 3.9 2.5 - - - -
119C THR* 2.8 36.6 + - - -
120C GLU 3.6 0.6 - - - -
121C GLU* 1.3 78.0 - - - +
123C ASN* 1.3 68.4 + - - -
321C VAL* 3.3 3.6 - - - +
359C PRO* 5.1 0.4 - - - -
361C ALA* 3.8 4.1 - - - +
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Residues in contact with ASN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLN* 2.8 29.2 + - - +
14A VAL* 4.4 3.8 - - - +
116C LYS* 4.0 18.4 - - + +
117C PHE 3.4 5.2 - - - +
118C TYR* 3.6 27.3 - - - -
122C GLY* 1.3 74.9 - - - -
124C TRP* 1.3 59.8 + - - +
319C VAL* 3.3 18.8 - - + +
320C LEU 4.1 6.2 - - - +
321C VAL* 3.8 6.5 - - - +
357C ASN 3.1 25.9 + - - -
358C CYS 3.9 2.8 + - - -
359C PRO* 3.4 30.5 - - - +
360C PHE 4.0 0.9 + - - -
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Residues in contact with TRP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PHE* 3.7 28.0 - + - -
81C LEU* 5.6 0.2 - - + -
116C LYS* 3.5 0.3 - - - -
117C PHE* 2.7 87.7 + + + -
119C THR* 5.0 1.6 - - - +
122C GLY 3.7 0.2 + - - -
123C ASN* 1.3 75.1 - - - +
125C ASP* 1.3 78.5 + - - +
126C PHE* 4.4 13.2 - + + -
201C PHE* 5.9 0.6 - - - -
203C TRP* 5.2 3.4 - + - -
215C LEU* 3.7 33.2 - - + -
217C TRP* 6.1 0.2 - + - -
260C LEU* 5.1 9.9 - - + -
317C PRO 5.1 0.2 + - - -
319C VAL 3.0 24.7 - - - -
320C LEU* 3.5 26.8 - - + +
321C VAL* 3.8 19.3 - - + +
324C MET* 3.7 22.0 - - + -
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Residues in contact with ASP 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLN* 5.3 0.5 + - - -
115C VAL 3.4 2.9 - - - +
116C LYS* 2.7 52.2 + - - +
124C TRP* 1.3 87.4 + - - +
126C PHE* 1.3 60.1 + - - +
127C VAL* 3.8 8.4 + - + -
201C PHE* 6.2 0.2 - - - -
314C GLY 3.9 0.3 - - - +
315C PHE* 3.2 9.9 - - + -
316C ASN 2.9 43.4 + - - +
317C PRO* 3.9 8.1 - - - +
319C VAL* 3.0 26.0 + - - +
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 3.2 31.2 - + + -
114C SER* 3.2 3.3 - - - -
115C VAL* 2.8 42.0 + - + +
117C PHE* 4.0 17.5 - - + -
124C TRP* 3.9 11.4 + + + +
125C ASP* 1.3 70.8 - - - +
127C VAL* 1.3 63.5 + - - +
128C GLY* 3.6 7.2 - - - -
196C SER* 3.7 24.0 - - - -
197C SER* 3.9 13.5 - - - -
201C PHE* 6.4 0.7 - + - -
215C LEU* 3.8 40.6 - - + -
217C TRP* 3.2 39.9 - + - +
260C LEU* 5.5 0.2 - - + -
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE 3.9 2.5 - - - -
114C SER* 3.4 15.3 - - - +
125C ASP* 3.8 4.5 + - + -
126C PHE* 1.3 82.2 - - - +
128C GLY* 1.3 57.4 + - - +
197C SER* 4.7 3.9 - - - +
201C PHE* 6.0 1.2 - - - -
315C PHE* 3.5 26.2 - - + -
316C ASN 3.8 3.4 - - - -
317C PRO* 3.5 33.8 - - + +
335C ARG* 3.1 39.6 + - - +
339C TYR* 3.9 11.9 - - + -
501C HEM 3.8 19.9 - - + +
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Residues in contact with GLY 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 2.5 43.9 + - - -
126C PHE* 3.6 7.6 - - - -
127C VAL* 1.3 74.6 - - - +
129C ASN* 1.3 57.6 + - - -
196C SER 3.1 18.4 - - - -
197C SER* 4.7 2.0 - - - -
501C HEM 3.3 19.8 - - - +
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Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C HIS* 3.5 16.5 + - - -
97C VAL* 5.3 0.6 - - - +
110C PRO* 3.8 19.5 - - + +
111C ARG 3.0 8.1 - - - +
112C GLY* 3.4 19.1 + - - -
113C PHE* 4.2 5.2 - - - +
128C GLY* 1.3 73.9 - - - +
130C ASN* 1.3 61.0 + - - +
131C LEU* 4.0 15.3 - - + +
133C VAL 5.6 0.4 + - - -
134C PHE* 3.8 24.5 - - - -
176C MET* 5.2 1.2 - - - +
195C GLY* 3.7 0.2 - - - -
196C SER* 2.7 35.6 + - - +
198C VAL* 4.5 1.9 - - + +
501C HEM 3.4 27.6 - - + +
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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