Contacts of the strand formed by residues 93 - 99 (chain K) 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 ALA 93 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47K ALA 3.5 12.6 - - - +
48K GLY* 3.9 3.1 - - - -
52K ASP* 4.1 5.4 - - + +
53K ALA* 3.7 34.8 - - - +
56K LEU* 3.7 9.4 - - + +
91K LEU 2.6 11.0 + - - +
92K GLU* 1.3 77.4 - - - +
94K MET* 1.3 71.7 + - - +
108K GLY 2.9 25.1 + - - -
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Residues in contact with MET 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K PHE* 3.3 4.3 - - - +
47K ALA 2.8 35.5 + - - +
56K LEU* 3.9 1.3 - - - +
93K ALA* 1.3 83.0 - - - +
95K LEU* 1.3 66.0 + - - +
105K ILE* 4.8 2.5 - - + -
106K ILE 3.2 11.4 - - - +
107K THR* 3.8 24.5 - - + -
123K ILE* 3.4 41.1 - - + +
124K GLY* 4.2 10.5 - - - +
22L LEU* 5.2 9.4 - - + -
27L MET* 4.6 15.9 - - + -
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Residues in contact with LEU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K ALA* 5.2 0.7 - - + -
45K GLY 3.0 8.5 - - - +
46K PHE* 3.1 33.7 - - + -
53K ALA 4.9 0.4 - - - +
56K LEU* 3.5 30.3 - - + +
57K PHE* 3.5 40.8 - - + +
60K PHE* 4.0 15.5 - - + -
94K MET* 1.3 75.1 - - - +
96K ILE* 1.3 63.8 + - - +
97K VAL* 4.0 17.7 - - + -
105K ILE* 3.3 10.9 - - - +
106K ILE* 2.8 37.4 + - + +
123K ILE* 4.0 0.8 - - - +
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Residues in contact with ILE 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K ILE* 3.6 36.3 - - + +
4K VAL* 4.5 1.3 - - - -
5K SER* 4.0 22.2 - - - -
14K VAL* 4.3 10.6 - - + +
43K LEU 3.4 1.4 - - - +
44K ALA* 3.1 4.3 - - - -
45K GLY 2.7 39.3 + - - +
95K LEU* 1.3 77.5 - - - +
97K VAL* 1.3 64.5 + - - +
98K ALA* 5.4 0.2 - - + -
103K SER* 5.3 1.1 - - - +
104K LEU 3.4 11.4 - - - +
105K ILE* 4.3 2.5 - - + -
121K LEU* 4.0 28.9 - - + +
122K ALA* 4.0 1.1 - - - -
123K ILE* 3.6 29.6 - - + +
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Residues in contact with VAL 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K VAL* 6.0 0.2 - - + -
43K LEU 2.9 7.6 - - - +
44K ALA* 4.2 10.1 - - + -
60K PHE* 3.4 34.1 - - + -
71K LEU* 3.9 24.6 - - + +
95K LEU* 4.0 16.8 - - + -
96K ILE* 1.3 80.2 - - - +
98K ALA* 1.3 59.2 + - - +
104K LEU* 2.5 59.6 + - + +
106K ILE* 4.1 12.8 - - + -
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Residues in contact with ALA 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K SER* 4.9 0.2 - - - +
12K VAL* 3.7 19.5 - - + -
14K VAL* 4.7 10.3 - - + -
42K VAL* 3.7 0.8 - - - -
43K LEU* 2.7 44.2 + - - +
71K LEU* 4.3 5.5 - - - +
96K ILE* 5.4 0.9 - - + -
97K VAL* 1.3 77.5 - - - +
99K ASP* 1.3 57.0 + - - +
102K GLU 3.1 18.8 - - - +
103K SER* 3.4 17.5 - - - +
172K LEU* 3.9 1.0 - - - +
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Residues in contact with ASP 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ARG* 2.9 7.6 + - - -
12K VAL* 3.8 2.6 - - - +
41K LYS 3.3 17.5 - - - +
42K VAL* 3.7 12.1 - - + -
69K GLY 4.6 5.4 - - - +
71K LEU* 3.6 23.8 + - - +
98K ALA* 1.3 74.3 - - - +
100K GLU* 1.3 68.3 + - - +
101K LYS* 3.7 8.7 + - - +
102K GLU* 2.6 47.7 + - - +
172K LEU* 3.3 12.3 - - - -
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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