Contacts of the strand formed by residues 308 - 312 (chain D) in PDB entry 5C5B
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 ASN 308 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D THR* 3.2 6.1 - - - -
305D GLN 2.8 37.0 + - - +
306D GLY* 2.7 29.7 + - - -
307D GLY* 1.3 83.5 + - - +
309D LEU* 1.3 60.6 + - - +
310D MET* 3.6 11.1 + - + +
321D LEU* 3.5 31.1 - - + +
323D GLN 3.9 2.7 - - - -
324D ASP* 3.3 21.0 + - - +
325D LEU* 3.8 4.3 - - - +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LEU* 6.1 0.2 - - + -
302D PHE* 4.3 8.7 - - + -
303D PHE 3.9 11.7 - - - +
304D THR* 4.1 8.5 - - + -
308D ASN* 1.3 70.7 - - - +
310D MET* 1.3 66.0 + - - +
321D LEU* 3.4 3.0 - - - +
322D ILE* 2.9 41.5 + - + +
323D GLN* 2.8 26.9 + - + +
325D LEU* 3.6 17.1 - - + +
344D ILE* 3.6 29.4 - - + -
353D ILE* 6.0 0.7 - - + -
355D LEU* 4.2 16.4 - - + -
366D TRP* 4.1 27.8 - - + -
370D ILE* 4.3 6.7 - - + -
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Residues in contact with MET 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D TYR 3.9 0.2 - - - +
302D PHE* 3.3 6.6 - - - +
303D PHE* 2.9 68.4 + - + +
305D GLN* 3.4 35.4 - - + +
308D ASN* 3.6 29.2 - - + +
309D LEU* 1.3 73.6 - - - +
311D CYS* 1.3 61.8 + - - +
312D GLN 4.3 0.2 - - - -
319D GLY 5.0 3.6 - - - +
320D GLY* 3.3 11.9 - - - +
321D LEU* 3.6 33.0 - - + -
322D ILE* 4.4 1.1 - - - -
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Residues in contact with CYS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D LEU* 5.7 0.7 - - - -
300D LEU* 3.5 42.0 - - - -
301D TYR 3.3 3.8 - - - -
302D PHE* 3.6 23.3 - - + -
303D PHE* 4.8 0.2 - - - -
310D MET* 1.3 73.7 - - - +
312D GLN* 1.3 63.1 + - - +
313D PRO* 3.7 8.7 - - - +
319D GLY* 4.2 0.7 - - - -
320D GLY* 2.7 32.4 + - - +
322D ILE* 3.8 16.7 - - + +
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Residues in contact with GLN 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C SER* 5.1 1.0 + - - -
17C PRO* 3.7 20.4 - - + +
18C GLN* 2.8 42.8 + - - +
301D TYR* 2.9 43.3 + - + +
303D PHE* 4.1 19.1 - - + -
310D MET 4.3 0.4 - - - -
311D CYS* 1.3 75.6 - - - +
313D PRO* 1.3 73.6 - - + +
316D ALA 2.7 24.8 + - - +
317D VAL 3.2 6.3 + - - -
318D ALA 3.9 4.7 - - - +
319D GLY* 3.5 22.0 + - - -
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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