Contacts of the strand formed by residues 69 - 74 (chain G) in PDB entry 1H4O
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 VAL 69 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LEU* 3.9 46.0 - - + +
29G PHE* 4.0 14.4 - - + -
32G LYS* 4.0 16.8 - - + +
33G LYS 3.8 0.2 + - - -
34G GLY* 3.1 15.1 - - - -
35G VAL 2.9 24.3 + - - -
67G VAL* 3.5 3.9 - - - +
68G GLN* 1.3 80.7 - - - +
70G VAL* 1.3 67.9 + - - +
71G ALA* 5.1 0.4 - - + -
95G ARG* 4.4 20.0 - - + +
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Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G VAL* 3.3 14.6 - - + +
37G PHE* 4.0 15.9 - - + -
55G PHE* 4.1 15.0 - - + -
59G ALA* 6.0 2.2 - - - +
62G LEU* 3.8 20.6 - - + -
67G VAL* 3.7 18.6 - - + +
69G VAL* 1.3 81.9 - - - +
71G ALA* 1.3 61.0 + - - +
93G LYS 3.9 14.3 + - - +
94G VAL* 3.5 21.9 - - + -
95G ARG* 2.9 27.6 + - - +
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Residues in contact with ALA 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LEU* 4.1 15.3 - - + -
29G PHE* 4.2 4.5 - - + -
35G VAL 2.9 6.7 + - - -
36G LEU* 3.3 14.2 - - + +
37G PHE* 2.9 31.8 + - - -
69G VAL* 4.2 0.9 - - + -
70G VAL* 1.3 76.2 - - - +
72G CYS* 1.3 60.9 + - - +
73G LEU 4.1 0.2 - - - -
94G VAL* 4.4 0.4 - - - -
95G ARG* 3.3 11.4 - - + +
97G LEU* 3.8 27.1 - - + -
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Residues in contact with CYS 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G PHE* 3.3 41.5 - - + -
39G VAL* 3.8 29.2 - - - -
52G LEU* 4.5 1.3 - - + -
71G ALA* 1.3 72.4 - - - +
73G LEU* 1.3 60.9 + - - +
74G SER* 5.4 0.4 - - - -
84G TRP* 4.0 17.3 - - - -
94G VAL* 3.9 10.3 - - + +
95G ARG 2.8 8.7 + - - +
96G LEU* 3.7 9.9 - - + +
97G LEU* 2.7 33.9 + - - +
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G VAL* 3.9 25.1 - - + -
25G LEU* 4.1 4.9 - - + -
36G LEU* 3.9 26.5 - - + -
37G PHE 2.8 12.7 + - - +
38G GLY* 3.4 3.0 - - - -
39G VAL* 3.0 26.0 + - - +
71G ALA 4.1 0.2 - - - -
72G CYS* 1.3 74.3 - - - +
74G SER* 1.3 62.0 + - - +
97G LEU* 3.4 29.6 - - + +
99G ASP* 4.2 12.1 - - + -
104G PHE* 3.7 44.4 - - + -
125G LEU* 3.7 12.5 - - + +
128G PHE* 4.6 2.2 - - + -
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Residues in contact with SER 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G VAL* 3.5 30.5 - - - -
41G GLY* 4.5 1.1 - - - -
42G ALA* 4.2 4.8 + - - +
72G CYS* 5.4 0.4 - - - -
73G LEU* 1.3 76.5 - - - +
75G VAL* 1.3 62.2 + - - +
76G ASN* 2.9 25.5 + - - -
81G THR* 3.6 17.0 - - - +
84G TRP* 5.1 2.6 - - - -
97G LEU 3.1 6.3 + - - -
98G ALA* 3.7 2.6 - - - -
99G ASP* 2.9 25.9 + - - -
125G LEU* 4.1 4.7 - - - -
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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