Contacts of the strand formed by residues 25 - 28 (chain P) 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 THR 25 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129K TYR* 3.1 32.5 - - + +
159K ILE* 3.0 13.5 - - + +
160K CYS* 5.4 0.2 - - - -
161K VAL* 4.1 0.7 - - - +
21P SER* 3.5 8.1 - - - -
22P LEU* 2.6 44.5 + - - +
24P ASN* 1.3 83.7 - - + +
26P VAL* 1.3 70.5 + - - +
27P MET 5.3 0.2 + - - -
128Q ASN* 3.7 25.9 + - - +
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Residues in contact with VAL 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158K ASP 3.6 22.7 - - - +
159K ILE* 3.0 23.0 + - - +
160K CYS 4.8 1.6 - - - +
161K VAL* 4.0 17.5 - - + +
19P GLN* 3.9 26.2 - - + +
20P VAL 3.8 6.3 - - - +
25P THR* 1.3 83.4 - - - +
27P MET* 1.3 63.2 + - - +
28P LYS 3.8 24.9 - - - +
29P GLY* 4.3 3.4 - - - +
128Q ASN* 5.1 3.5 - - - +
131Q LEU* 5.2 3.3 - - - +
135Q ARG* 4.6 10.9 + - - -
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Residues in contact with MET 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P VAL* 3.0 35.8 + - + +
22P LEU* 4.3 37.2 - - + +
25P THR 4.1 1.2 + - - -
26P VAL* 1.3 72.6 - - - +
28P LYS* 1.3 62.8 + - + +
50P THR* 4.7 8.7 - - + -
94Q MET* 5.7 3.1 - - - +
105Q ILE* 4.4 23.3 - - + -
107Q THR* 5.9 3.6 - - + -
111Q ASP* 5.6 2.9 - - - +
113Q VAL* 4.2 31.6 - - + +
128Q ASN* 6.1 0.2 - - - -
131Q LEU* 6.1 1.2 - - - +
135Q ARG* 4.8 8.4 + - - -
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Residues in contact with LYS 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLY 3.5 0.3 - - - +
19P GLN* 3.6 0.3 - - - -
20P VAL* 2.6 46.2 + - + +
26P VAL* 3.4 7.2 - - - +
27P MET* 1.3 86.4 - - + +
29P GLY* 1.3 59.0 + - - +
30P ASN* 3.6 35.6 + - - +
31P ALA* 3.8 11.4 - - + +
113Q VAL* 4.4 4.7 - - + -
114Q GLN* 2.5 40.3 + - - +
115Q PRO 3.8 11.5 + - - -
116Q GLU* 5.1 4.3 - - + +
135Q ARG* 6.0 0.9 - - - +
444W LEU* 3.1 35.8 + - + +
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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
------------------------------------------------------------
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