Contacts of the strand formed by residues 307 - 312 (chain A) in PDB entry 1L9N
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 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ASP* 3.5 3.2 + - - +
305A ASN* 3.0 18.0 + - - +
306A LEU* 1.3 79.3 - - - +
308A VAL* 1.3 63.9 + - - +
309A ASP* 4.5 4.0 + - - +
324A ASP* 3.3 0.5 - - - +
395A ASP* 3.4 13.4 + - - +
397A ILE* 3.5 31.5 - - - +
452A PHE* 5.8 0.7 - - - -
703A CA 2.1 33.6 - - - -
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 3.9 15.9 - - + -
300A HIS 3.7 27.8 - - - +
301A ASP* 4.0 6.5 - - + -
307A SER* 1.3 80.6 + - - +
309A ASP* 1.3 65.1 + - - +
324A ASP* 3.8 13.7 - - + +
325A SER 4.4 1.8 - - - +
326A VAL* 3.8 18.6 - - + -
394A ALA* 4.5 2.0 - - + -
395A ASP 2.9 13.6 + - - +
396A ARG* 3.6 5.3 - - + +
397A ILE* 2.9 26.0 + - - +
418A ILE* 3.4 25.1 - - + -
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 5.1 6.4 - - - +
307A SER* 4.5 3.1 + - - +
308A VAL* 1.3 78.0 - - - +
310A VAL* 1.3 66.6 + - - +
311A TYR* 3.6 30.8 + - + -
322A GLY* 4.9 6.2 + - - -
324A ASP* 4.4 24.6 - - + +
325A SER* 5.4 1.2 - - - -
397A ILE* 3.4 20.8 - - - +
399A TRP* 2.7 32.7 + - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASP* 1.3 78.3 - - - +
311A TYR* 1.3 66.4 + - - +
312A TYR* 4.3 8.5 - - + +
325A SER* 6.0 0.9 - - - -
326A VAL* 4.3 20.6 - - + +
396A ARG* 3.5 43.5 - - + +
397A ILE 3.0 14.0 + - - +
398A THR* 3.6 19.3 - - + +
399A TRP* 2.9 26.9 + - - +
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Residues in contact with TYR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASP* 3.6 33.0 + - + +
310A VAL* 1.3 80.1 - - - +
312A TYR* 1.3 66.5 - - - +
318A PRO* 3.7 1.4 - - - +
319A LEU* 2.8 53.7 + - + +
321A LYS* 3.6 37.2 - - + -
322A GLY* 4.0 21.5 - - - -
399A TRP* 3.5 22.0 - + + -
401A TYR* 3.9 11.0 - - + -
408A GLN* 3.1 38.4 + - + -
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Residues in contact with TYR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL* 4.3 12.2 - - + +
311A TYR* 1.3 79.2 - - - +
313A ASP* 1.3 59.7 + - - +
316A GLY 4.6 0.4 - - - -
317A ASN 3.2 9.4 - - - +
318A PRO* 3.6 24.7 - - + -
319A LEU* 3.7 5.6 - - - -
396A ARG* 4.2 2.8 + - - -
398A THR* 4.1 25.1 - - + -
399A TRP 3.1 7.7 + - - +
400A LEU* 3.3 13.4 - - + -
401A TYR* 2.7 30.7 + - - +
570A ARG* 4.7 12.0 + - + -
572A THR* 3.4 40.7 + - + -
574A VAL* 4.7 5.8 - - + -
584A VAL* 4.2 8.1 - - + -
586A GLU* 2.6 38.6 + - + +
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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