Contacts of the strand formed by residues 61 - 69 (chain A) in PDB entry 2OG9
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 GLN 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TRP* 4.7 1.8 - - - -
53A GLU* 4.4 16.4 + - - +
54A ILE 3.2 11.0 - - - +
55A GLU* 2.7 33.2 + - + +
59A GLY 4.0 2.4 + - - +
60A HIS* 1.3 77.6 - - - +
62A GLY* 1.3 68.6 + - - +
129A LEU* 3.5 14.0 - - - -
132A LYS* 3.5 30.9 + - + +
384A ARG* 4.1 8.9 - - - +
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Residues in contact with GLY 62 (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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52A ALA 3.8 0.2 - - - +
53A GLU* 3.4 5.9 - - - +
54A ILE* 2.8 32.5 + - - +
61A GLN* 1.3 82.6 - - - +
63A LEU* 1.3 60.3 + - - +
125A ALA* 3.4 23.1 - - - -
128A ASP* 3.4 9.0 - - - -
129A LEU* 3.9 5.3 - - - +
132A LYS* 4.6 0.7 - - - -
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Residues in contact with LEU 63 (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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51A PHE* 4.1 16.4 - - + -
52A ALA 3.4 14.8 - - - +
53A GLU* 3.9 17.9 - - + -
61A GLN* 6.1 0.9 - - + -
62A GLY* 1.3 73.5 - - - +
64A GLY* 1.3 68.6 + - - +
65A PHE* 6.0 1.8 - - + -
125A ALA* 3.5 10.3 - - - +
128A ASP* 2.8 24.0 + - - +
132A LYS* 5.1 2.5 - - - +
344A PHE* 5.1 3.6 - - + -
363A LEU* 3.7 12.9 - - + +
365A LEU* 3.6 37.2 - - + +
366A THR* 4.2 4.5 - - - +
367A LEU* 3.9 30.5 - - + -
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Residues in contact with GLY 64 (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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51A PHE* 3.5 7.1 - - - -
52A ALA 3.0 27.9 + - - -
63A LEU* 1.3 77.1 - - - +
65A PHE* 1.3 69.6 + - - +
121A ALA 3.4 18.6 - - - -
124A VAL* 3.6 9.2 - - - -
125A ALA* 3.5 8.8 - - - +
363A LEU* 4.8 0.2 - - - -
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Residues in contact with PHE 65 (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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49A ILE* 4.1 13.0 - - + -
50A LEU 3.0 14.1 - - - +
51A PHE* 3.8 18.6 - + + -
63A LEU* 6.0 2.0 - - + -
64A GLY* 1.3 80.5 - - - +
66A SER* 1.3 70.9 + - - +
120A GLY 4.5 0.2 - - - +
121A ALA* 3.8 14.8 + - - +
124A VAL* 4.1 13.4 - - + +
290A PRO* 4.1 20.1 - - + +
316A PHE* 4.9 5.2 - + - -
317A ALA* 4.2 28.0 - - + -
319A GLU* 5.2 3.1 - - + -
320A LEU* 4.8 13.8 - - + +
340A LEU* 4.4 18.6 - - + -
343A LEU* 6.4 0.4 - - + -
344A PHE* 4.1 24.7 - + - -
363A LEU* 4.9 9.2 - - + -
365A LEU* 4.2 16.4 - - + -
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Residues in contact with SER 66 (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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49A ILE* 3.7 6.6 - - - +
50A LEU* 2.9 39.1 + - - +
65A PHE* 1.3 77.7 - - - +
67A TYR* 1.3 67.5 + - - +
76A GLN* 3.1 18.3 + - - -
117A GLN 3.2 29.9 + - - -
120A GLY 5.0 0.2 - - - -
121A ALA* 4.0 4.3 - - - +
290A PRO* 3.9 20.9 - - - -
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.2 4.7 - - + -
48A ALA 3.2 12.6 - - - +
49A ILE* 3.8 16.4 - - + -
65A PHE* 5.3 2.2 - + + -
66A SER* 1.3 80.9 + - - +
68A SER* 1.3 73.0 + - - +
69A LYS* 3.6 31.4 + - + +
76A GLN* 3.0 19.1 + - - -
117A GLN* 4.3 4.7 + - - +
288A ASP* 2.4 36.2 + - - -
290A PRO* 3.8 17.9 + - + +
291A ARG* 2.7 32.0 + - + -
315A HIS* 4.8 1.0 - - - -
316A PHE* 3.2 42.2 - + + +
108B SER* 4.4 3.7 + - - +
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Residues in contact with SER 68 (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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47A ILE* 3.6 4.2 - - - +
48A ALA* 3.0 28.3 + - - +
67A TYR* 1.3 76.9 - - - +
69A LYS* 1.3 60.3 + - - +
70A ARG 3.8 7.8 + - - +
72A GLY* 3.1 24.1 - - - -
73A GLY* 3.3 23.6 + - - -
76A GLN* 3.0 25.5 + - - -
114A LEU* 4.7 0.3 - - - +
117A GLN* 4.7 0.7 + - - -
108B SER* 3.5 10.6 + - - -
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Residues in contact with LYS 69 (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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44A MSE 3.7 37.7 - - + -
46A GLU 5.2 0.2 - - - -
47A ILE* 4.3 13.9 - - + -
67A TYR* 3.6 28.4 + - + -
68A SER* 1.3 70.1 - - - +
70A ARG* 1.3 75.2 + - + +
71A ALA 4.3 0.9 - - - +
291A ARG* 3.9 11.1 - - - +
315A HIS* 4.3 20.4 + - - -
316A PHE* 4.6 14.3 - - - -
337A PHE* 6.0 0.4 - - - -
339A TRP* 4.3 15.5 - - - -
107B ALA* 5.0 0.7 + - - +
108B SER* 3.2 26.2 + - - +
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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