Contacts of the strand formed by residues 338 - 344 (chain A) in PDB entry 6KSF
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 ARG 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASN 3.8 0.7 - - - +
221A TYR* 3.7 2.1 - - - -
222A TYR* 2.9 74.3 + - + +
228A LEU* 5.9 0.4 - - - +
247A SER* 2.7 35.7 + - - +
248A PHE 3.5 10.8 - - - +
250A GLN 3.3 25.1 - - - +
251A SER 4.5 0.7 - - - -
252A ALA* 3.6 23.2 - - - +
270A MET* 3.5 23.9 - - - +
289A VAL* 4.0 16.0 - - - +
292A VAL* 4.3 16.0 - - + +
337A ALA* 1.3 76.1 - - - +
339A VAL* 1.3 67.4 + - - +
340A ASN* 3.0 29.8 + - - +
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Residues in contact with VAL 339 (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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115A VAL* 5.5 4.0 - - + -
118A CYS* 3.9 33.7 - - + -
119A LEU* 4.3 12.8 - - + -
219A LEU* 5.5 0.7 - - + -
220A ASN 3.4 7.2 - - - +
221A TYR* 4.1 23.6 - - + -
246A PHE 3.8 0.2 - - - +
247A SER* 3.4 5.2 + - - -
248A PHE* 2.9 48.2 + - + +
333A TYR* 4.3 4.0 - - + -
334A LEU* 4.0 22.2 - - + -
338A ARG* 1.3 79.5 - - - +
340A ASN* 1.3 69.5 + - - +
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Residues in contact with ASN 340 (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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218A ILE 3.6 0.7 - - - +
219A LEU* 3.2 7.4 - - - +
220A ASN* 2.9 42.9 + - + +
222A TYR* 4.2 7.9 - - + +
245A SER* 3.2 24.7 + - - -
246A PHE 3.1 15.7 - - - +
247A SER* 4.0 1.6 - - - -
270A MET* 4.9 4.5 - - - +
338A ARG* 3.0 35.4 + - - +
339A VAL* 1.3 75.7 - - - +
341A MET* 1.3 68.8 + - - +
342A THR* 3.3 20.4 + - - -
403A SIN 5.5 4.8 + - - +
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Residues in contact with MET 341 (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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114A TRP* 4.8 6.7 - - + +
118A CYS* 3.5 28.3 - - - -
122A TYR* 4.8 3.8 - - - -
196A LEU* 3.6 35.9 - - + -
199A LEU* 4.2 6.7 - - + -
218A ILE 3.5 3.6 - - - -
219A LEU* 3.7 18.2 - - + -
244A LEU 3.5 0.7 - - - +
245A SER* 3.1 6.4 - - - -
246A PHE* 2.8 65.0 + - + -
248A PHE* 3.6 27.1 - - + -
339A VAL* 5.1 0.2 - - + -
340A ASN* 1.3 76.8 + - - +
342A THR* 1.3 62.6 + - - +
343A VAL* 4.3 1.1 - - + -
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Residues in contact with THR 342 (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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216A ALA 4.4 0.4 - - - -
217A GLY* 3.0 7.3 - - - -
218A ILE* 2.9 48.6 + - + +
219A LEU* 5.0 0.5 - - - +
220A ASN* 4.6 0.7 + - - -
243A LEU* 4.1 19.7 - - + -
244A LEU 3.2 7.4 - - - +
245A SER* 4.1 3.1 + - - -
340A ASN* 3.3 19.8 + - - -
341A MET* 1.3 71.1 + - - +
343A VAL* 1.3 67.7 + - - +
344A ARG* 3.8 25.8 - - - +
403A SIN 4.1 22.1 + - + +
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Residues in contact with VAL 343 (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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192A PHE* 4.2 16.8 - - + -
196A LEU* 4.2 15.9 - - + -
200A SER* 3.6 23.3 - - - +
212A PHE* 3.9 14.4 - - + -
214A ALA* 3.5 31.6 - - + -
216A ALA 3.5 3.1 - - - -
217A GLY* 5.0 0.2 - - - -
242A PRO 4.1 1.4 - - - +
243A LEU* 3.4 6.8 - - - +
244A LEU* 2.9 39.8 + - + +
246A PHE* 4.6 9.0 - - + -
341A MET* 5.0 1.6 - - + -
342A THR* 1.3 81.7 - - - +
344A ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 344 (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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184A TYR* 3.7 16.6 + - - -
212A PHE* 4.1 8.1 - - - -
214A ALA* 3.9 0.3 - - - -
215A GLU 2.9 23.7 + - - -
216A ALA* 2.9 21.9 + - + +
218A ILE* 3.7 23.6 - - - +
233A ASP* 3.0 26.3 + - - -
237A LEU* 4.0 15.2 - - + +
242A PRO 4.5 3.6 - - - -
243A LEU* 3.4 22.1 - - + +
283A ARG* 5.1 4.0 - - - +
342A THR* 3.8 8.9 - - + +
343A VAL* 1.3 78.1 - - - +
345A GLN* 1.3 65.3 + - - +
346A VAL* 4.5 6.7 - - + -
401A CL 3.3 19.4 - - - +
403A SIN 2.9 28.7 + - - -
101B XL3 3.5 17.6 - - - +
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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