Contacts of the strand formed by residues 103 - 107 (chain H) in PDB entry 1G3I
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 SER 103 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H SER* 4.3 11.4 + - - -
7H ARG* 3.8 19.3 + - - +
12H VAL* 4.5 2.1 - - - +
96H ILE* 5.2 0.2 - - - +
98H ALA* 3.4 17.6 - - - +
102H GLU* 1.3 82.6 + - - +
104H LEU* 1.3 70.0 + - - +
115H PRO* 3.2 23.1 - - - +
119H GLN* 4.3 13.8 + - - +
121H LEU* 3.4 19.2 - - - +
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Residues in contact with LEU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ILE* 5.3 1.6 - - + -
71H LEU* 3.5 24.0 - - + -
72H LEU* 3.6 32.8 - - + -
75H ALA* 3.8 21.8 - - + -
96H ILE* 3.3 5.4 - - - -
97H VAL* 2.6 45.0 + - + +
102H GLU* 4.3 6.1 - - - +
103H SER* 1.3 87.6 - - - +
105H ILE* 1.3 64.6 + - - +
106H ILE* 5.1 1.3 - - + -
112H VAL* 4.9 11.4 - - + -
113H VAL 3.6 15.3 - - - +
114H GLN* 4.2 15.9 - - + -
115H PRO* 5.0 0.2 - - + -
121H LEU* 3.4 11.4 - - - +
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Residues in contact with ILE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H MET* 4.9 4.9 - - - -
95H LEU 3.1 15.0 - - - +
96H ILE* 4.2 5.2 - - + -
104H LEU* 1.3 79.0 - - - +
106H ILE* 1.3 65.2 + - - +
107H THR* 5.2 2.9 - - + +
111H ASP 3.7 1.2 - - - +
112H VAL* 3.6 2.6 - - - -
113H VAL* 3.0 56.7 + - + +
121H LEU* 4.4 18.2 - - + -
122H ALA 4.4 6.7 - - - +
123H ILE* 3.2 30.7 - - + -
27I MET* 4.4 23.8 - - + -
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H LEU* 4.1 6.9 - - + +
60H PHE* 3.6 39.5 - - + -
75H ALA* 3.8 20.9 - - + +
78H LEU* 4.5 20.6 - - + -
79H ALA* 5.5 2.0 - - + -
82H TRP* 5.4 1.1 - - + -
94H MET* 3.3 3.7 - - - +
95H LEU* 2.7 45.9 + - + +
97H VAL* 4.1 17.7 - - + -
104H LEU* 5.1 0.4 - - + -
105H ILE* 1.3 78.2 - - - +
107H THR* 1.3 77.3 + - - +
110H GLY* 5.7 0.2 - - - -
111H ASP 3.5 12.3 - - - +
112H VAL* 4.4 9.0 - - + -
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Residues in contact with THR 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H LEU* 4.5 2.5 - - - -
82H TRP* 4.5 4.2 - - - -
93H ALA 3.8 4.7 - - - -
94H MET* 3.8 26.5 - - - -
105H ILE* 5.2 4.9 - - + +
106H ILE* 1.3 90.9 - - - +
108H GLY* 1.3 59.9 + - - +
109H ILE* 2.9 22.7 - - + +
110H GLY* 3.1 13.7 + - - -
111H ASP* 2.1 40.7 + - - +
113H VAL* 5.8 4.7 - - + -
27I MET* 5.3 7.9 - - + -
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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