Contacts of the strand formed by residues 2269 - 2275 (chain A) in PDB entry 4NFA
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 SER2269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2254A ILE* 5.5 0.7 - - - -
2255A THR 3.1 12.8 - - - -
2256A LEU* 3.6 18.4 - - - -
2257A PHE* 4.3 3.8 - - - -
2267A LEU 3.6 1.0 + - - -
2268A PRO* 1.3 78.0 - - - +
2270A THR* 1.3 66.7 + - - +
2280A GLN* 3.2 28.9 + - - +
2283A ILE* 4.2 9.7 - - - +
2284A ALA* 5.0 1.0 + - - -
2287A LEU* 3.4 19.5 - - - +
2402A GOL 4.9 5.6 + - - -
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Residues in contact with THR2270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2253A GLU 5.6 0.2 - - - +
2254A ILE* 3.2 6.8 - - - +
2255A THR* 2.8 51.8 + - + +
2257A PHE* 4.2 13.7 - - + -
2269A SER* 1.3 78.1 + - - +
2271A ILE* 1.3 64.6 + - - +
2272A GLN* 5.3 0.7 - - + +
2280A GLN* 3.7 6.5 - - - -
2283A ILE* 6.3 0.4 - - - -
2402A GOL 5.0 5.9 + - - -
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Residues in contact with ILE2271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2252A PHE* 3.8 26.5 - - + -
2253A GLU 3.4 8.5 - - - +
2254A ILE* 3.9 9.9 - - + -
2270A THR* 1.3 82.6 + - - +
2272A GLN* 1.3 71.0 + - - +
2273A ASN* 4.0 6.3 + - + +
2278A THR* 3.8 35.7 - - + +
2279A SER* 4.1 1.1 - - - -
2280A GLN* 3.5 35.2 + - + +
2283A ILE* 4.1 11.4 - - + -
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Residues in contact with GLN2272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2252A PHE* 3.3 2.9 - - - -
2253A GLU* 2.8 57.1 + - + +
2270A THR* 5.3 0.8 - - + +
2271A ILE* 1.3 74.8 - - - +
2273A ASN* 1.3 63.5 + - - +
2274A HIS* 3.4 35.7 + - + +
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Residues in contact with ASN2273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251A LYS 3.7 2.9 - - - +
2252A PHE* 3.7 16.3 - - - +
2271A ILE* 3.9 7.6 + - + -
2272A GLN* 1.3 78.1 - - - +
2274A HIS* 1.3 71.2 + - - +
2275A VAL 4.0 5.9 - - - +
2276A GLY 2.9 25.7 + - - +
2277A ASN* 4.5 1.6 - - - +
2278A THR* 3.4 35.0 + - - +
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Residues in contact with HIS2274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2242A LEU* 4.5 8.3 - - + +
2251A LYS* 2.9 47.4 + - + +
2252A PHE* 4.3 3.4 - - - -
2253A GLU* 4.6 2.4 + - - +
2272A GLN* 3.4 50.5 + - + -
2273A ASN* 1.3 78.5 + - - +
2275A VAL* 1.3 71.1 + - + +
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Residues in contact with VAL2275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2249A PHE* 3.7 48.0 - - + +
2250A ALA* 3.4 5.7 - - - +
2251A LYS* 2.9 43.3 + - + +
2252A PHE* 5.3 0.2 - - - -
2273A ASN* 4.0 3.3 - - - +
2274A HIS* 1.3 91.9 - - + +
2276A GLY* 1.3 65.8 + - - +
2278A THR* 5.3 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