Contacts of the strand formed by residues 316 - 325 (chain A) in PDB entry 3KYS
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 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A PRO* 5.1 1.1 - - - -
254A LYS* 4.7 20.0 - - - +
312A CYS* 4.1 2.9 - - - -
313A SER* 2.7 40.8 + - - +
314A PHE* 3.4 0.8 - - + -
315A GLY* 1.3 83.7 - - - +
317A GLN* 1.3 57.4 + - - +
318A VAL 3.4 1.2 + - - -
58B ARG* 4.5 24.2 - - - +
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Residues in contact with GLN 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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252A PRO* 4.5 12.0 - - + +
310A LYS* 3.6 32.4 - - + +
311A VAL 3.3 12.1 - - - +
312A CYS* 3.6 19.2 - - - +
315A GLY 4.3 0.8 + - - -
316A LYS* 1.3 68.7 - - - +
318A VAL* 1.3 66.3 + - - +
319A VAL 3.4 0.6 - - - -
320A GLU* 3.2 45.0 + - - +
58B ARG* 4.0 9.1 + - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 2.7 18.6 + - + +
312A CYS 4.5 0.2 - - - -
313A SER* 3.5 25.6 - - - +
316A LYS 3.4 0.4 + - - -
317A GLN* 1.3 72.1 - - - +
319A VAL* 1.3 59.1 + - + +
346A TYR* 3.7 17.3 - - + +
56B HIS 4.1 1.2 - - - +
58B ARG* 3.3 50.6 + - + +
61B SER* 3.7 30.7 - - - -
64B ASP* 3.3 27.4 - - - +
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Residues in contact with VAL 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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309A THR 3.8 0.9 - - - +
310A LYS* 3.2 2.8 - - - -
311A VAL* 2.9 40.8 + - + +
317A GLN* 3.7 4.3 - - - +
318A VAL* 1.3 88.6 - - + +
320A GLU* 1.3 62.5 + - - +
344A P1L 3.8 26.5 - - + -
346A TYR* 4.1 23.1 - - + -
55B VAL* 3.7 28.5 - - + -
56B HIS 3.3 4.5 - - - +
57B VAL* 4.0 25.4 - - + -
61B SER* 4.8 0.9 - - - -
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Residues in contact with GLU 320 (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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308A SER* 3.1 26.4 + - - +
309A THR 3.5 3.1 - - - -
310A LYS* 3.9 9.2 - - + +
317A GLN* 3.2 28.1 + - - +
319A VAL* 1.3 74.9 - - - +
321A LYS* 1.3 59.2 + - - +
322A VAL* 3.8 16.8 - - + +
55B VAL* 3.4 0.3 - - - -
56B HIS* 2.5 71.0 + - + +
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Residues in contact with LYS 321 (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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293A VAL* 5.1 4.2 - - - +
307A CYS 3.6 2.3 - - - +
308A SER* 3.4 1.8 - - - -
309A THR* 2.7 50.7 + - - +
319A VAL* 4.7 0.2 - - - +
320A GLU* 1.3 73.3 - - - +
322A VAL* 1.3 63.2 + - - +
323A GLU* 3.5 24.6 + - + +
341A SER* 2.7 22.8 + - - -
342A PRO 2.8 20.2 + - - -
344A P1L 3.6 43.6 - - + +
53B GLN* 3.3 31.9 - - + +
54B ILE 3.6 2.5 - - - +
55B VAL* 3.9 14.4 - - + +
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Residues in contact with VAL 322 (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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306A THR* 3.8 25.4 - - + +
307A CYS 3.5 2.7 - - - -
308A SER* 4.0 9.6 - - - +
320A GLU* 3.8 22.9 - - - +
321A LYS* 1.3 74.8 - - - +
323A GLU* 1.3 63.7 - - - +
324A THR* 4.7 6.7 - - - +
52B HIS 3.1 3.8 - - - +
53B GLN* 3.6 1.2 - - - -
54B ILE* 2.8 51.7 + - + +
56B HIS* 3.9 16.2 - - + -
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Residues in contact with GLU 323 (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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293A VAL* 5.8 2.6 - - - +
306A THR* 3.4 2.1 - - - -
307A CYS* 2.6 53.8 + - + +
309A THR* 4.7 6.1 + - - +
321A LYS* 3.5 25.6 + - + +
322A VAL* 1.3 78.0 - - - +
324A THR* 1.3 61.5 - - - +
325A GLU 4.0 0.7 + - - -
338A ILE* 3.5 33.3 - - + +
341A SER* 3.1 35.7 + - - -
52B HIS 3.2 7.5 - - - +
53B GLN* 3.5 14.9 + - - +
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Residues in contact with THR 324 (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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304A THR* 4.4 3.4 - - + -
305A VAL 3.6 5.2 - - - +
306A THR* 3.6 17.3 + - - +
322A VAL* 4.7 7.1 - - - +
323A GLU* 1.3 73.8 - - - +
325A GLU* 1.3 65.9 + - - +
326A TYR* 3.8 22.6 - - + +
379A ARG* 3.5 28.9 + - - +
51B GLY* 3.4 26.0 + - - -
52B HIS* 3.2 28.4 + - - +
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Residues in contact with GLU 325 (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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305A VAL* 2.6 50.9 + - + +
307A CYS* 4.9 0.7 - - - -
323A GLU 4.0 0.2 + - - -
324A THR* 1.3 80.9 - - - +
326A TYR* 1.3 80.2 + - - +
336A TYR* 3.8 11.2 - - + -
337A ARG 3.2 41.3 + - - +
338A ILE* 3.6 25.6 - - + +
51B GLY* 4.3 10.9 - - - -
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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