Contacts of the helix formed by residues 297 - 302 (chain A) in PDB entry 1ML3
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 VAL 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A LEU* 1.3 79.4 - - - +
298A SER* 1.3 67.7 - - - +
299A ALA 4.2 1.8 - - - +
300A ASP* 2.9 21.1 + - - +
301A PHE* 3.4 8.0 - - - -
332A TRP* 4.1 3.8 - - - -
212B ARG* 4.0 16.8 - - + +
215B ARG* 3.3 46.7 - - + +
220B ASN* 3.7 27.1 - - - +
221B ILE 3.8 10.8 - - - +
222B ILE* 3.8 23.8 - - + -
223B PRO* 4.6 0.2 - - - -
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Residues in contact with SER 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A THR* 4.6 3.4 - - - +
254A ASP 4.9 2.8 + - - -
255A VAL* 3.5 34.4 - - - +
297A VAL* 1.3 71.8 - - - +
299A ALA* 1.3 64.2 + - - +
301A PHE 3.0 12.3 + - - -
302A ILE* 5.0 0.2 - - - -
332A TRP* 3.5 26.8 - - - -
219B VAL 4.1 2.6 + - - -
220B ASN* 3.2 10.9 + - - -
221B ILE* 2.9 39.2 + - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.0 3.7 + - + -
298A SER* 1.3 81.4 + - - +
300A ASP* 1.3 59.3 + - - +
301A PHE 3.1 4.4 + - - -
302A ILE* 3.3 33.2 + - + +
215B ARG* 4.7 1.6 - - - +
219B VAL 5.1 1.8 - - - +
220B ASN* 3.1 19.3 + - - +
53C ASP 5.2 2.7 - - - +
54C THR* 3.8 37.9 - - + +
58C LYS* 5.4 0.3 - - - -
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 3.5 21.6 - - + +
297A VAL* 2.9 25.4 + - - +
299A ALA* 1.3 77.1 - - - +
301A PHE* 1.3 62.1 + - - +
302A ILE 3.5 0.4 - - - -
304A ASP* 5.4 0.2 - - - +
215B ARG* 2.7 46.2 + - - -
52C TYR* 2.9 33.3 - - + +
53C ASP 4.2 3.1 + - - +
58C LYS* 2.8 37.5 + - - +
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Residues in contact with PHE 301 (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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255A VAL* 4.1 13.0 - - + -
292A THR* 4.0 6.7 - - + -
296A LEU* 3.6 36.8 - - + -
297A VAL 3.4 19.3 - - - -
298A SER 3.0 8.4 + - - +
300A ASP* 1.3 80.3 - - - +
302A ILE* 1.3 67.0 + - - +
303A ASN 3.1 0.7 + - - -
304A ASP* 3.1 28.8 + - + +
309A ILE* 3.6 41.1 - - + -
332A TRP* 3.3 61.7 - + + -
334A ASP* 3.4 12.0 - - - +
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Residues in contact with ILE 302 (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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55A VAL* 3.6 43.5 - - + +
56A HIS* 4.1 1.3 - - - +
253A PRO* 6.6 0.2 - - + -
254A ASP* 4.8 2.9 - - - +
255A VAL* 3.8 17.0 - - + -
298A SER 3.8 0.4 + - - -
299A ALA* 3.3 32.9 + - + +
300A ASP 3.5 3.0 - - - +
301A PHE* 1.3 79.1 + - - +
303A ASN* 1.3 87.6 + - - +
304A ASP 3.5 0.2 + - - -
334A ASP* 3.3 6.3 - - - +
54C THR 5.1 5.6 - - - +
58C LYS* 5.1 6.2 + - - -
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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