Contacts of the strand formed by residues 87 - 95 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D VAL* 3.1 29.5 - - + +
66D PHE 3.1 4.7 - - - -
67D LYS* 3.2 41.1 + - + +
85D GLY 3.4 1.5 + - - +
86D THR* 1.3 76.9 + - - +
88D VAL* 1.3 65.1 + - - +
89D PRO* 4.3 3.9 - - - +
120D GLU* 5.2 2.1 - - - +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 3.5 4.6 - - - -
66D PHE* 2.7 47.1 + - + +
80D PHE* 3.6 39.3 - - + -
86D THR* 4.1 6.7 - - - +
87D GLU* 1.3 79.0 - - - +
89D PRO* 1.4 77.6 - - + +
90D VAL* 4.0 2.0 - - + -
117D PHE* 3.5 37.7 - - + -
118D TYR 4.3 8.1 - - - +
119D THR* 4.6 2.7 - - - +
120D GLU* 4.4 4.9 - - - +
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Residues in contact with PRO 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLY 3.7 8.7 - - - +
65D VAL* 4.6 2.5 - - + -
87D GLU 4.3 3.8 - - - +
88D VAL* 1.4 85.3 - - - +
90D VAL* 1.3 62.3 + - - +
118D TYR* 3.0 59.1 + - + +
360D PHE* 5.5 9.4 - - + -
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D HIS* 3.6 7.4 + - - +
64D GLY* 2.9 53.9 + - - +
65D VAL* 3.5 8.1 - - - +
66D PHE* 4.0 9.4 - - + -
88D VAL 3.8 7.4 - - - +
89D PRO* 1.3 79.1 - - - +
91D PHE* 1.3 61.2 + - - +
115D VAL* 3.8 13.9 - - + -
116D LYS 3.1 12.8 - - - +
117D PHE* 3.8 26.2 - - + -
118D TYR* 4.0 4.9 - - - -
297D MET* 4.1 18.8 - - - -
299D LEU* 4.2 4.9 - - + -
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLY* 3.9 8.1 - - - -
62D ALA 3.3 28.0 - - - -
63D HIS* 3.5 26.7 - + - +
90D VAL* 1.3 75.0 - - - +
92D ALA* 1.3 66.5 + - - +
93D ARG* 4.9 1.1 - - + -
115D VAL* 3.5 1.1 - - - -
116D LYS* 2.8 36.9 + - + -
118D TYR* 3.6 21.6 - - + +
303D VAL* 3.7 15.9 - - + -
309D GLU* 3.8 17.7 - - + -
310D THR* 3.6 31.9 - - - -
313D VAL* 4.0 22.4 - - + -
315D PHE* 3.6 8.5 - + - -
356D ILE* 3.8 13.7 - - + -
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE 4.5 0.2 - - - -
61D GLY* 3.0 3.5 - - - -
62D ALA 2.9 36.3 + - - +
90D VAL* 4.3 0.4 - - + -
91D PHE* 1.3 79.2 - - - +
93D ARG* 1.3 61.5 + - - +
94D PHE* 4.2 21.7 - - + -
114D SER 3.0 12.3 - - - +
115D VAL* 4.1 13.7 - - + -
297D MET* 4.6 2.7 - - - -
299D LEU* 4.2 19.0 - - + +
315D PHE* 4.5 0.2 - - - -
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Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ARG* 3.5 26.4 - - - +
56D HIS 2.9 22.0 + - - -
57D ALA 2.8 29.5 + - - -
59D GLY* 3.8 13.4 - - - +
60D PHE 3.1 15.5 - - - +
61D GLY* 4.4 2.0 - - - -
91D PHE* 4.9 1.1 - - + -
92D ALA* 1.3 76.1 - - - +
94D PHE* 1.3 67.7 + - - +
95D SER* 3.7 11.9 + - - -
112D GLY 4.1 1.0 - - - +
113D PHE* 4.0 0.9 + - - -
114D SER* 2.9 34.3 + - - -
306D TYR* 4.8 3.8 + - - -
310D THR* 3.5 34.6 + - + +
311D GLU* 4.8 1.8 + - - -
313D VAL* 4.2 4.9 - - + -
315D PHE* 3.8 13.4 - - + -
501D HEM 2.8 42.0 + - - +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLY* 2.9 3.6 - - - -
60D PHE* 2.7 51.6 + + - +
61D GLY* 5.7 0.2 - - - -
62D ALA 5.9 0.4 - - - -
92D ALA* 4.2 15.9 - - + -
93D ARG* 1.3 77.1 - - - +
95D SER* 1.3 61.2 + - - +
112D GLY 3.4 8.3 - - - +
113D PHE* 3.6 37.5 - + - -
114D SER 5.1 0.2 - - - -
190D TYR* 3.6 38.9 - - + -
193D MET* 3.4 18.8 - - + -
246D THR* 5.3 2.7 - - + -
258D TRP* 3.6 26.9 - + - -
297D MET* 4.5 1.6 - - + -
299D LEU* 3.6 27.6 - - + -
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D HIS* 2.7 30.2 + - - +
58D ARG 2.9 20.6 - - - -
59D GLY* 4.0 1.6 - - - -
93D ARG* 3.7 17.8 + - - -
94D PHE* 1.3 76.0 - - - +
96D THR* 1.3 63.4 + - - +
111D ARG* 3.1 13.3 - - - +
112D GLY* 2.7 36.9 + - - -
190D TYR* 3.9 7.1 - - - -
501D HEM 4.2 4.6 + - - +
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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