Contacts of the strand formed by residues 69 - 77 (chain A) in PDB entry 2O6F
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 CYS 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A TYR* 4.3 11.4 - - + -
49A PHE 3.2 15.9 - - - +
51A PRO* 3.7 12.6 - - - -
67A ALA* 3.6 3.2 - - - +
68A ASP* 1.3 78.9 - - - +
70A HIS* 1.3 58.2 + - - +
71A ILE* 3.8 22.0 - - - -
128A ASN* 3.4 3.1 - - - -
129A VAL* 2.8 38.0 + - - +
131A PHE* 3.6 30.5 - - - -
180A TRP* 4.7 2.7 - - + -
185A TRP* 3.9 12.8 - - + -
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Residues in contact with HIS 70 (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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48A TYR* 3.0 7.1 - - - +
49A PHE* 2.8 63.2 + + + -
50A GLN 3.7 16.4 - - - +
51A PRO* 4.0 1.2 - - + +
52A VAL* 3.5 8.2 - - + +
54A MET* 3.9 9.4 - - - -
69A CYS* 1.3 73.0 - - - +
71A ILE* 1.3 68.9 + - - +
72A GLU* 4.3 0.2 - - + -
117A MET* 3.7 18.8 - - - -
124A HIS* 3.1 24.7 + - - -
127A ALA* 3.3 31.3 + - - -
128A ASN* 2.9 23.4 + - - +
155B HIS* 3.7 2.2 + + - -
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Residues in contact with ILE 71 (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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33A ILE* 3.4 32.3 - - + -
47A VAL 3.5 2.0 - - - +
48A TYR* 4.2 6.3 - - + -
69A CYS* 3.8 14.6 - - - -
70A HIS* 1.3 79.6 - - - +
72A GLU* 1.3 63.7 + - - +
101A LEU* 4.6 15.0 - - + -
114A PHE* 3.7 25.7 - - + -
126A GLY* 3.2 3.8 - - - -
127A ALA 2.8 33.7 + - - +
129A VAL* 4.0 21.1 - - + -
131A PHE* 4.1 23.3 - - + -
140A VAL* 5.5 2.9 - - + -
142A PHE* 3.9 9.9 - - + -
178A PHE* 6.0 1.1 - - + -
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Residues in contact with GLU 72 (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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30A GLU* 4.1 8.6 - - - +
45A GLY 3.7 0.3 - - - +
46A GLY* 3.4 5.2 - - - -
47A VAL* 2.8 49.3 + - + +
49A PHE* 3.3 24.4 - - + -
70A HIS* 4.2 0.6 - - + -
71A ILE* 1.3 78.1 - - - +
73A ALA* 1.3 59.5 + - - +
74A ASP* 2.4 37.8 + - - +
119A ALA* 5.3 0.5 - - - +
121A ASP* 4.4 12.6 - - - +
124A HIS* 3.3 41.6 + - + +
125A TYR 3.6 3.8 - - - -
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Residues in contact with ALA 73 (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 VAL* 5.1 0.4 - - + -
45A GLY 3.4 5.6 - - - +
72A GLU* 1.3 72.1 - - - +
74A ASP* 1.3 62.7 - - - +
75A ILE* 3.8 15.8 + - + -
97A VAL* 4.5 3.1 - - + -
114A PHE* 4.0 12.9 - - + -
124A HIS* 3.6 3.5 - - - +
125A TYR* 2.8 45.1 + - + +
142A PHE* 3.5 29.4 - - + -
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Residues in contact with ASP 74 (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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30A GLU* 5.0 2.1 - - - +
43A HIS 3.5 1.5 - - - +
44A VAL* 3.3 6.2 - - - -
45A GLY* 2.8 40.9 + - - +
47A VAL* 4.3 14.9 - - - +
72A GLU* 2.4 38.8 - - - +
73A ALA* 1.3 72.0 - - - +
75A ILE* 1.3 61.5 + - - +
76A HIS* 4.2 19.2 + - + +
123A PRO 4.7 2.3 - - - +
124A HIS* 3.4 10.5 - - - +
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Residues in contact with ILE 75 (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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42A LEU* 3.9 29.8 - - + -
43A HIS 3.4 3.1 - - - +
44A VAL* 4.4 9.4 - - + -
73A ALA* 3.8 15.9 + - + +
74A ASP* 1.3 80.1 - - - +
76A HIS* 1.3 70.8 + - - +
91A PHE* 3.5 13.4 - - - -
92A VAL* 3.2 21.5 + - + -
95A LEU* 3.8 20.0 - - + -
97A VAL* 3.7 19.7 - - + -
125A TYR* 3.7 31.4 - - + -
144A ILE* 4.0 21.3 - - + -
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Residues in contact with HIS 76 (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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42A LEU* 3.6 3.1 - - - -
43A HIS* 2.8 45.2 + - + +
74A ASP* 4.2 16.4 + - + +
75A ILE* 1.3 87.0 + - - +
77A ALA* 1.3 64.0 + - - +
89A GLY* 3.4 23.5 + - - +
90A ASP 3.1 7.2 - - - +
91A PHE* 3.3 35.2 + + + -
92A VAL* 3.9 5.6 - - - -
123A PRO 5.2 5.5 + - - -
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Residues in contact with ALA 77 (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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41A PRO 3.5 10.3 - - - +
43A HIS* 5.1 1.1 - - - +
76A HIS* 1.3 74.1 - - - +
78A ASN* 1.3 65.7 + - - +
81A GLY* 4.2 4.9 - - - -
86A TYR* 3.6 32.8 - - + -
87A GLY 3.7 12.1 - - - +
88A VAL* 3.8 1.6 - - - +
89A GLY* 2.7 29.5 + - - +
90A ASP 2.9 9.8 + - - +
92A VAL* 3.5 11.7 - - + +
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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