Contacts of the strand formed by residues 238 - 244 (chain 4) in PDB entry 1G6Q
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 LYS 238 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2364 ALA 4.1 1.2 + - - +
2374 PHE* 1.3 75.5 - - - +
2394 SER* 1.4 59.6 + - - +
3064 GLU* 4.5 26.9 + - + +
3074 LEU 3.9 2.5 - - - -
3084 VAL* 3.9 30.1 - - + +
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Residues in contact with SER 239 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2224 LEU* 2.9 49.5 + - - +
2234 ILE* 3.7 8.0 - - - +
2374 PHE* 3.4 22.0 - - - +
2384 LYS* 1.4 73.5 + - - +
2404 ASN* 1.3 63.7 + - - +
3064 GLU* 3.4 3.2 - - - -
3074 LEU 2.9 39.6 + - - +
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Residues in contact with ASN 240 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2204 ASP* 4.2 3.1 - - - +
2214 LYS 4.8 6.9 - - - +
2224 LEU* 4.8 2.9 - - - +
2394 SER* 1.3 75.6 - - - +
2414 PHE* 1.3 59.2 + - - +
2424 LYS* 3.6 23.8 + - - +
3044 GLU* 5.4 1.0 - - - +
3054 GLY* 2.7 27.3 + - - +
3064 GLU* 3.5 27.9 - - - +
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Residues in contact with PHE 241 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704 LEU* 3.9 37.2 - - + -
2204 ASP* 3.2 13.7 - - - +
2224 LEU* 3.7 20.2 - - + -
2404 ASN* 1.3 74.1 - - - +
2424 LYS* 1.3 77.8 + - - +
2434 LEU* 4.0 16.2 - - + -
2544 ILE* 4.4 4.5 - - + -
3034 ILE* 3.5 28.3 - - + -
3044 GLU* 3.5 1.0 - - - -
3054 GLY* 2.8 46.8 + - - -
3064 GLU 3.4 19.5 - - - -
3074 LEU* 3.6 20.6 - - + -
3234 ILE* 4.2 17.7 - - + -
3244 SER 4.5 0.2 - - - -
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Residues in contact with LYS 242 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2184 THR* 4.1 4.9 + - - -
2204 ASP* 3.0 29.6 + - - +
2404 ASN* 3.6 25.6 - - - +
2414 PHE* 1.3 104.1 + - - +
2434 LEU* 1.3 66.0 + - - +
2444 THR* 5.6 0.4 - - - +
3034 ILE 3.4 5.4 - - - +
3044 GLU* 4.3 23.5 + - + +
3054 GLY 5.2 0.2 - - - +
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Residues in contact with LEU 243 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704 LEU* 3.6 12.3 - - + +
1714 ALA* 3.9 5.2 - - - -
1724 GLY* 3.7 24.0 - - - +
2174 THR* 3.7 11.0 - - - +
2184 THR* 3.0 22.2 - - - +
2204 ASP* 3.5 27.1 - - + +
2414 PHE* 4.0 13.2 - - + -
2424 LYS* 1.3 81.0 - - - +
2444 THR* 1.3 62.8 + - - +
2544 ILE* 4.0 17.7 - - + -
3014 ASP 3.9 0.2 - - - +
3024 THR* 3.5 3.8 - - - -
3034 ILE* 2.8 59.5 + - + +
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Residues in contact with THR 244 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2174 THR* 3.3 3.3 - - - -
2184 THR* 2.8 46.2 + - + +
2424 LYS 5.6 0.2 - - - -
2434 LEU* 1.3 75.0 + - - +
2454 ALA* 1.3 67.9 + - - +
2464 LYS 3.5 0.3 + - - -
3004 GLY* 3.6 28.0 - - - +
3014 ASP 3.5 2.9 - - - -
3024 THR* 3.9 11.8 - - + +
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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
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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