Contacts of the strand formed by residues 87 - 95 (chain A) 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 GLU 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL* 3.4 30.8 - - + +
66A PHE 3.1 5.4 - - - +
67A LYS* 3.2 28.4 + - + +
85A GLY 3.6 12.6 - - - +
86A THR* 1.3 76.0 + - - +
88A VAL* 1.3 62.6 + - - +
89A PRO* 4.3 4.2 - - - +
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Residues in contact with VAL 88 (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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65A VAL* 3.4 3.6 - - - -
66A PHE* 2.7 55.8 + - + +
68A VAL* 5.3 0.2 - - + -
80A PHE* 3.7 35.0 - - + -
86A THR* 4.9 3.4 - - - +
87A GLU* 1.3 77.4 - - - +
89A PRO* 1.3 80.4 - - + +
90A VAL* 3.4 0.9 + - - +
117A PHE* 4.0 14.8 - - + -
118A TYR 3.6 25.1 - - - +
119A THR* 4.3 6.5 - - - +
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Residues in contact with PRO 89 (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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64A GLY 3.6 9.4 - - - +
65A VAL* 4.5 3.1 - - + -
87A GLU 4.3 3.6 - - - +
88A VAL* 1.3 88.8 - - - +
90A VAL* 1.3 58.3 + - - +
118A TYR* 3.0 56.8 + - + +
360A PHE* 5.5 10.1 - - + -
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Residues in contact with VAL 90 (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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63A HIS* 3.5 6.3 + - - +
64A GLY* 2.9 51.8 + - - +
65A VAL 3.7 7.0 - - - +
66A PHE* 3.8 10.1 - - + -
88A VAL 3.8 7.0 - - - +
89A PRO* 1.3 80.0 - - - +
91A PHE* 1.3 60.3 + - - +
115A VAL* 3.7 14.1 - - + -
116A LYS 3.0 11.7 - - - +
117A PHE* 3.7 29.2 - - + -
118A TYR* 4.1 4.7 - - - -
297A MET* 4.0 23.6 - - + -
299A LEU* 4.2 3.8 - - + -
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Residues in contact with PHE 91 (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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61A GLY* 4.0 7.6 - - - -
62A ALA 3.4 20.0 - - - -
63A HIS* 3.4 31.6 - + - +
90A VAL* 1.3 75.2 - - - +
92A ALA* 1.3 68.9 + - - +
93A ARG* 5.0 0.7 - - + -
115A VAL* 3.6 1.7 - - - -
116A LYS* 2.9 34.3 + - + +
118A TYR* 3.6 22.7 - - + +
303A VAL* 3.6 32.1 - - + -
309A GLU* 3.8 18.2 - - + -
310A THR* 3.9 19.3 - - - -
313A VAL* 3.9 24.9 - - + -
315A PHE* 3.8 4.0 - + - -
356A ILE* 3.7 14.8 - - + -
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Residues in contact with ALA 92 (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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60A PHE 4.5 0.2 - - - -
61A GLY* 2.9 4.3 - - - -
62A ALA 2.8 37.4 + - - +
91A PHE* 1.3 80.1 - - - +
93A ARG* 1.3 60.8 + - - +
94A PHE* 4.2 10.5 - - + -
114A SER 3.1 11.0 - - - +
115A VAL* 4.0 14.4 - - + -
297A MET* 4.5 0.9 - - - -
299A LEU* 4.0 29.6 - - + +
315A PHE* 4.6 0.4 - - - -
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Residues in contact with ARG 93 (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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53A ARG* 3.2 41.3 - - - +
56A HIS 2.9 22.4 + - - -
57A ALA 2.9 28.7 + - - -
59A GLY* 3.5 14.8 - - - +
60A PHE 3.2 9.2 - - - +
61A GLY* 4.4 1.8 - - - -
91A PHE* 5.0 0.9 - - + -
92A ALA* 1.3 74.5 - - - +
94A PHE* 1.3 67.7 - - - +
95A SER* 3.4 11.3 + - - -
112A GLY 4.0 0.9 - - - +
113A PHE* 3.9 1.0 + - - -
114A SER* 2.8 36.8 + - - -
306A TYR* 4.5 4.4 + - - -
310A THR* 3.6 26.7 + - + +
311A GLU* 4.7 1.8 + - - -
313A VAL* 4.2 5.2 - - + -
315A PHE* 3.8 13.6 - - + -
501A HEM 3.1 29.4 + - - +
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Residues in contact with PHE 94 (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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59A GLY* 3.0 2.3 - - - -
60A PHE* 2.7 50.5 + + - +
62A ALA 6.1 0.7 - - - -
92A ALA* 4.2 14.1 - - + -
93A ARG* 1.3 76.8 - - - +
95A SER* 1.3 62.2 + - - +
112A GLY 3.2 9.2 - - - +
113A PHE* 3.7 41.7 - + - -
114A SER 4.8 1.1 - - - -
190A TYR* 3.6 37.6 - - + -
193A MET* 3.4 20.2 - - + -
246A THR* 5.2 2.9 - - + -
258A TRP* 3.6 27.6 - + - -
297A MET* 4.6 1.3 - - + -
299A LEU* 3.6 27.8 - - + -
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Residues in contact with SER 95 (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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56A HIS* 2.7 28.9 + - - +
58A ARG 3.1 18.6 - - - -
59A GLY* 3.9 0.9 - - - -
93A ARG* 3.4 21.5 + - - -
94A PHE* 1.3 77.6 - - - +
96A THR* 1.3 63.9 - - - +
111A ARG* 3.3 11.8 - - - +
112A GLY* 2.8 30.9 + - - -
190A TYR* 3.9 8.7 - - - -
501A HEM 4.2 4.9 + - - +
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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