Contacts of the strand formed by residues 314 - 319 (chain A) in PDB entry 2K6D
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A ALA* 5.8 2.0 - - - +
282A ASN 4.7 6.9 + - - -
283A ASP* 4.7 19.9 + - - +
285A GLU 4.6 12.5 + - - -
286A LEU* 3.5 13.9 - - + +
287A THR* 4.3 19.0 + - - +
310A GLU* 2.8 30.4 - - - +
311A LEU 2.9 12.6 + - - +
312A ASN* 3.6 13.4 - - + +
313A GLY* 1.3 85.2 - - - +
315A ARG* 1.3 64.6 + - - +
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Residues in contact with ARG 315 (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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283A ASP 5.3 1.7 - - - +
284A ASP* 4.0 8.5 - - - +
285A GLU 5.0 0.7 - - - +
286A LEU* 4.4 2.5 - - - -
297A ILE* 3.5 37.6 - - + +
298A ASN* 5.8 2.8 - - - +
308A GLU* 3.0 43.0 + - - +
309A GLY 3.9 3.3 + - - -
310A GLU* 4.0 16.2 - - - +
314A ARG* 1.3 82.7 + - - +
316A GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 316 (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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284A ASP 3.5 9.6 - - - -
286A LEU* 3.3 36.3 - - - +
308A GLU* 3.6 9.3 + - - -
309A GLY 3.4 23.0 + - - -
315A ARG* 1.3 75.4 - - - +
317A VAL* 1.3 63.7 + - - -
318A PHE* 4.0 1.4 - - - -
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Residues in contact with VAL 317 (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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284A ASP 4.9 0.2 - - - +
285A GLU* 3.8 13.5 - - + +
286A LEU 3.8 10.8 + - - +
306A TRP* 3.7 30.1 - - + -
307A TRP 3.1 17.5 - - - +
308A GLU* 3.5 23.3 - - + +
316A GLY* 1.3 73.3 - - - -
318A PHE* 1.3 62.6 + - - +
74B ARG* 3.2 39.0 - - + +
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Residues in contact with PHE 318 (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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274A VAL* 5.4 1.8 - - + -
286A LEU* 3.8 33.0 - - + +
288A ILE* 4.3 29.6 - - + -
294A VAL* 4.8 11.0 - - + -
296A LEU* 5.5 2.5 - - + -
305A GLY 3.8 0.4 - - - +
306A TRP* 4.3 3.6 - - - -
307A TRP* 3.3 26.5 + + + -
308A GLU* 4.2 2.2 - - - -
309A GLY* 3.8 26.9 - - - -
316A GLY 4.0 1.6 - - - -
317A VAL* 1.3 82.0 - - - +
319A PRO* 1.3 81.5 - - + +
320A ASP* 2.9 30.4 - - + +
323A VAL* 4.7 7.4 - - + -
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Residues in contact with PRO 319 (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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278A TYR* 5.0 6.3 - - + -
281A GLN* 5.3 4.0 - - - +
285A GLU* 5.5 1.3 - - - +
288A ILE* 5.7 1.2 - - - +
305A GLY* 2.8 16.2 - - - +
306A TRP* 3.8 15.7 - - + -
317A VAL 4.7 0.4 - - - +
318A PHE* 1.3 92.3 - - + +
320A ASP* 1.3 59.3 + - - +
321A ASN* 3.1 9.2 + - + +
322A PHE* 3.5 31.8 + - + +
323A VAL* 3.9 1.9 - - - +
8B LEU* 6.3 0.7 - - + -
70B VAL* 3.3 44.0 - - + -
76B CYS* 4.5 3.6 - - - +
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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