Contacts of the strand formed by residues 17 - 22 (chain E) in PDB entry 2IFG
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 17 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A GLU* 3.7 18.8 + - - +
15E CYS 3.9 3.3 + - - -
16E ASP* 1.3 74.4 - - - +
18E VAL* 1.3 64.1 + - - +
56E THR* 3.8 18.2 - - - +
57E LYS 3.2 16.6 - - - -
59E ARG* 3.5 16.8 + - - +
108E CYS* 3.7 18.6 - - - -
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Residues in contact with VAL 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLU* 5.1 4.0 - - - -
17E SER* 1.3 81.1 - - - +
19E SER* 1.3 71.8 - - - +
20E VAL* 4.1 15.6 + - + +
55E GLU 3.8 1.2 - - - +
56E THR* 3.3 2.1 - - - -
57E LYS* 3.0 46.8 + - + +
58E CYS 4.2 0.2 - - - +
59E ARG* 3.7 37.5 - - - +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLU* 5.4 3.5 + - - -
350A GLN* 5.0 5.7 + - - -
378A PHE 5.2 2.1 - - - +
379A MET* 3.3 36.5 - - - +
18E VAL* 1.3 74.2 - - - +
20E VAL* 1.3 68.9 + - - +
54E PHE* 3.9 12.4 - - - -
55E GLU 3.1 8.5 - - - -
56E THR* 3.1 24.4 + - - +
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A MET* 4.8 6.7 - - - -
18E VAL* 4.1 18.4 - - + +
19E SER* 1.3 81.0 - - - +
21E TRP* 1.3 65.2 + - - +
22E VAL* 4.2 19.5 - - + -
54E PHE* 3.8 6.5 - - - -
55E GLU* 2.8 40.0 + - + +
57E LYS* 4.5 16.8 - - - +
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Residues in contact with TRP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A THR* 4.4 1.8 - - + +
353A HIS* 3.2 35.5 + + - -
379A MET* 3.6 24.5 - - + +
380A ASP 4.0 11.7 - - - -
382A PRO* 4.5 28.0 - - + +
20E VAL* 1.3 75.2 - - - +
22E VAL* 1.3 62.5 + - - +
23E GLY 3.8 2.6 + - - -
52E TYR* 4.5 10.5 - + + -
53E PHE 3.4 25.4 - - - -
54E PHE* 3.8 32.1 - + + -
31F ILE* 4.2 17.5 - - + -
86F PHE* 4.6 5.2 - - + -
101F PHE* 3.3 56.5 - + - -
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E VAL* 4.2 11.7 - - + -
21E TRP* 1.3 72.8 - - - +
23E GLY* 1.3 60.1 + - - +
24E ASP* 3.8 16.8 - - - +
25E LYS* 4.0 34.8 - - + +
51E GLN 4.2 0.2 - - - +
52E TYR* 3.5 2.8 - - - -
53E PHE* 2.7 44.6 + - + +
55E GLU* 3.4 35.7 - - + +
57E LYS* 6.0 1.6 - - - +
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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