Contacts of the strand formed by residues 207 - 211 (chain 6) in PDB entry 3EXG
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 ILE 207 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2066 HIS* 1.3 81.1 - - - +
2086 THR* 1.3 72.1 + - - +
2096 VAL* 4.2 5.2 - - + -
2316 VAL* 4.9 1.3 - - + -
2326 GLU 3.4 2.1 + - - +
2336 CYS* 3.2 27.9 - - + +
2346 GLU 2.8 23.7 + - - -
2566 THR* 3.4 13.0 - - - +
2586 HIS* 3.5 24.2 - - + +
2596 LEU 4.4 0.2 - - - +
2606 VAL* 3.8 25.1 - - + -
3236 ILE* 3.9 26.7 - - + -
3266 THR* 3.9 11.9 - - + -
3276 LEU* 4.1 11.0 - - + -
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Residues in contact with THR 208 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2076 ILE* 1.3 72.9 - - - +
2096 VAL* 1.3 61.1 + - - +
2106 VAL* 4.0 13.2 - - + -
2346 GLU* 3.6 4.5 - - - +
2366 ILE* 3.7 23.8 - - + -
2496 ILE* 4.7 1.8 - - + +
2526 SER* 2.4 33.8 + - - +
2536 VAL* 4.1 10.1 - - + -
2566 THR* 2.7 19.8 + - - +
2586 HIS 3.1 15.7 + - - -
2596 LEU* 3.4 6.2 - - + +
2606 VAL 3.0 25.6 + - - -
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Residues in contact with VAL 209 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2076 ILE* 4.2 5.6 - - + -
2086 THR* 1.3 76.0 - - - +
2106 VAL* 1.3 57.9 + - - +
2116 SER 4.1 0.2 + - - -
2196 CYS* 3.8 32.5 - - + +
2336 CYS* 3.7 21.8 - - + -
2346 GLU 2.8 12.2 + - - +
2356 VAL* 3.3 10.2 - - + +
2366 ILE* 2.7 32.2 + - - -
2606 VAL* 3.5 10.8 - - + +
2626 VAL* 4.0 10.3 - - + -
3196 ILE* 4.8 6.1 - - + -
3236 ILE* 3.7 28.0 - - + -
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Residues in contact with VAL 210 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2086 THR* 4.0 11.4 - - + -
2096 VAL* 1.3 74.2 - - - +
2116 SER* 1.3 66.6 + - - +
2366 ILE* 3.6 12.1 - - + +
2386 MET* 3.6 26.3 - - + +
2496 ILE* 3.9 33.0 - - + -
2596 LEU* 3.4 28.3 - - + -
2606 VAL 3.0 7.6 + - - +
2616 THR* 3.3 6.0 - - + -
2626 VAL* 2.9 23.7 + - - +
2756 ILE* 3.9 13.9 - - + -
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Residues in contact with SER 211 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2096 VAL 4.1 0.4 + - - -
2106 VAL* 1.3 78.7 - - - +
2126 HIS* 1.3 74.2 + - - +
2156 PRO* 4.0 2.9 - - - +
2166 VAL* 3.6 22.5 + - - +
2196 CYS* 3.9 23.6 - - - -
2356 VAL* 6.2 1.3 - - - -
2366 ILE 3.0 9.6 + - - +
2386 MET* 3.0 32.7 + - - +
2626 VAL* 2.7 24.3 + - - +
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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