Contacts of the helix formed by residues 305 - 312 (chain I) in PDB entry 1MKD
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 SER 305 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301I HIS* 5.5 0.4 - - - -
304I VAL* 1.3 76.1 - - - +
306I ASN* 1.3 64.8 + - - +
307I GLN* 3.5 10.3 + - - +
308I PHE* 3.0 18.5 + - - +
309I LEU* 3.0 22.7 + - - +
326I LEU* 4.2 4.0 - - - -
440I GLN* 3.0 24.2 + - - -
452I SER* 5.4 0.3 + - - -
3009I ZAR 6.1 0.7 - - - -
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Residues in contact with ASN 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305I SER* 1.3 72.7 - - - +
307I GLN* 1.3 57.5 + - - +
309I LEU* 3.1 8.4 + - - +
310I ILE* 2.8 41.0 + - + +
324I SER* 4.2 3.4 - - - +
325I VAL* 3.4 16.1 - - + +
326I LEU* 2.8 43.5 + - - +
327I GLU* 2.9 31.1 + - - -
369I ASP* 4.1 11.7 + - - -
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Residues in contact with GLN 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305I SER* 3.1 8.9 - - - +
306I ASN* 1.3 79.1 - - - +
308I PHE* 1.3 57.2 + - - +
310I ILE* 3.2 21.1 + - - +
311I ASN* 2.8 70.8 + - - +
452I SER* 5.9 2.9 - - - +
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Residues in contact with PHE 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304I VAL* 3.5 22.4 - - + -
305I SER* 3.0 26.1 + - - +
307I GLN* 1.3 76.8 - - - +
309I LEU* 1.3 61.7 + - + +
311I ASN* 3.2 5.9 + - - +
312I THR* 2.8 67.3 + - + +
440I GLN* 3.8 14.4 - - + +
443I ARG* 3.3 51.1 - - + -
444I GLU* 3.6 39.7 - - + +
447I ARG* 4.0 8.3 - - - -
449I MET* 4.3 6.5 - - + -
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Residues in contact with LEU 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302I PRO* 4.6 5.8 - - + -
304I VAL* 3.9 21.3 - - + -
305I SER 3.0 16.4 + - - +
306I ASN* 3.4 8.3 - - - +
308I PHE* 1.3 78.7 - - + +
310I ILE* 1.3 60.7 + - - +
312I THR* 3.5 3.7 + - - +
313I ASN 3.4 1.2 + - - -
314I SER* 2.7 56.0 + - - +
316I LEU* 4.5 11.4 - - + -
317I ALA* 3.4 6.8 - - + +
325I VAL* 4.1 17.0 - - + -
326I LEU* 3.6 38.8 - - + -
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Residues in contact with ILE 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I ASN* 2.8 27.3 + - + +
307I GLN* 3.6 26.0 - - - +
309I LEU* 1.3 77.2 - - - +
311I ASN* 1.3 66.2 + - - +
313I ASN* 3.0 20.8 + - - +
317I ALA* 3.9 9.8 - - + +
322I ASP* 3.5 60.3 - - + +
325I VAL* 4.3 5.8 - - + -
358J ARG* 5.4 0.9 - - - +
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Residues in contact with ASN 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307I GLN* 2.8 54.5 + - - +
308I PHE* 3.9 1.7 - - - +
310I ILE* 1.3 78.9 - - - +
312I THR* 1.3 59.8 + - - +
313I ASN* 3.1 11.8 + - - +
444I GLU* 5.7 1.2 + - - -
449I MET* 3.8 25.8 - - + +
452I SER* 6.0 0.6 + - - -
355J GLN* 5.2 6.2 - - - +
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Residues in contact with THR 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308I PHE* 2.8 58.4 + - + +
309I LEU* 3.5 11.3 + - - +
311I ASN* 1.3 75.0 - - - +
313I ASN* 1.3 73.1 + - - +
314I SER* 3.3 8.1 + - - -
447I ARG* 4.1 17.0 - - - +
449I MET* 3.8 24.0 - - + -
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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