Contacts of the strand formed by residues 95 - 99 (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 ARG 95 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLU* 2.7 44.1 + - - +
23G VAL* 4.3 9.7 - - - +
28G LEU* 3.5 29.6 - - + +
69G VAL* 4.4 16.7 - - + +
70G VAL 2.9 16.0 + - - +
71G ALA* 3.3 9.7 - - + +
72G CYS 2.8 29.1 + - - +
93G LYS 6.0 0.4 - - - -
94G VAL* 1.3 74.7 - - - +
96G LEU* 1.3 61.3 + - - +
97G LEU* 3.7 9.0 + - + -
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Residues in contact with LEU 96 (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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15G PHE 3.9 0.2 - - - +
16G GLU* 3.5 29.9 + - - +
17G GLY 4.5 2.3 + - - +
52G LEU* 4.3 7.4 - - + -
72G CYS* 3.7 19.5 - - + +
81G THR* 3.8 24.1 + - - +
82G GLY* 5.3 2.5 - - - -
84G TRP* 3.7 33.2 - - + -
85G GLY* 3.7 20.9 - - - -
90G ALA* 3.6 21.1 - - + -
94G VAL* 3.4 20.8 + - + +
95G ARG* 1.3 71.4 - - - +
97G LEU* 1.3 60.1 + - - +
98G ALA 4.2 0.2 + - - -
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Residues in contact with LEU 97 (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* 4.1 11.9 - - + -
15G PHE 3.3 8.7 - - - +
16G GLU* 4.2 17.7 - - + -
23G VAL* 4.3 16.4 - - + -
25G LEU* 3.6 31.4 - - + -
28G LEU* 3.7 17.7 - - + -
71G ALA* 3.8 10.5 - - + -
72G CYS 2.7 17.5 + - - +
73G LEU* 3.4 17.8 - - + +
74G SER* 3.1 27.0 + - - +
81G THR* 4.5 3.6 - - - +
95G ARG* 4.2 12.6 - - + +
96G LEU* 1.3 80.2 - - - +
98G ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 98 (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* 3.3 4.9 - - - +
15G PHE* 2.8 38.1 + - + +
74G SER 3.7 4.5 - - - -
76G ASN 3.3 17.3 - - - +
77G ASP 3.8 0.7 - - - -
78G ALA* 3.6 22.0 - - + +
81G THR* 3.5 23.1 + - + +
96G LEU 4.2 0.2 + - - -
97G LEU* 1.3 72.9 - - - +
99G ASP* 1.3 58.5 + - - +
100G PRO* 3.4 10.0 - - + +
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Residues in contact with ASP 99 (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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12G VAL* 4.7 0.3 - - - +
13G GLU 4.8 2.8 - - - +
14G VAL* 4.0 22.0 - - + +
73G LEU* 4.2 9.9 - - + -
74G SER 2.9 17.2 + - - +
75G VAL* 3.4 16.8 - - + +
98G ALA* 1.3 72.5 - - - +
100G PRO* 1.3 68.5 - - - +
101G THR* 4.2 3.1 + - - -
102G GLY* 3.0 15.3 + - - -
103G ALA* 3.0 28.1 + - - +
104G PHE* 2.8 35.6 + - - +
105G GLY 4.1 0.9 + - - -
125G LEU* 5.3 3.0 - - + +
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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