Contacts of the strand formed by residues 299 - 304 (chain A) in PDB entry 1LC7
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 TYR 299 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.4 29.6 - - - +
155A PRO* 3.7 12.8 - - - +
156A ASN 2.7 24.0 + - - -
157A ASN* 4.0 8.6 - - - -
158A PRO 3.6 18.4 - - - -
160A GLY* 3.4 30.4 - - - -
188A PHE* 3.6 36.0 - + - -
295A GLY* 4.0 9.7 - - - -
297A ALA* 3.2 19.0 + - + +
298A ASN* 1.3 91.7 - - - +
300A LEU* 1.3 73.8 + - - +
337A ARG* 3.8 12.8 - - + -
338A VAL 3.3 11.9 - - - +
340A ILE* 3.8 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO 4.6 0.4 - - - -
159A THR 5.5 0.2 - - - -
280A PHE* 4.1 17.5 - - + -
281A TYR* 4.0 29.6 - - + -
284A LEU* 3.5 27.1 - - + -
292A VAL* 4.2 10.3 - - + -
293A TYR 3.5 19.5 - - - +
295A GLY* 3.6 20.4 - - - +
299A TYR* 1.3 84.0 - - - +
301A LEU* 1.3 60.9 + - - +
302A LEU* 3.8 2.0 + - + -
337A ARG* 3.4 6.6 - - - -
338A VAL* 3.0 39.5 + - + +
340A ILE* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TRP* 4.3 5.6 - - + -
158A PRO* 3.4 27.1 + - + +
159A THR* 4.0 35.5 + - + +
292A VAL* 3.6 2.8 - - - +
293A TYR* 3.0 59.0 + - + -
300A LEU* 1.3 72.7 - - - +
302A LEU* 1.3 60.8 + - - +
325A CYS* 4.0 20.0 - - - -
331A LEU* 4.5 6.7 - - + -
335A TYR* 4.0 26.7 - - + -
336A TYR 3.3 17.0 - - - +
337A ARG* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.4 12.6 - - + -
290A LEU* 4.2 19.3 - - + -
291A THR 3.4 2.7 - - - +
292A VAL* 3.7 37.5 - - + -
293A TYR* 5.0 0.4 - - - -
300A LEU* 4.2 9.9 - - + +
301A LEU* 1.3 76.5 - - - +
303A ARG* 1.3 61.9 + - - +
304A CYS 4.1 0.7 - - - +
311A LEU* 5.1 3.6 - - + -
322A ILE* 5.7 1.1 - - + -
334A ARG 3.7 0.3 - - - +
335A TYR* 3.4 8.7 - - - -
336A TYR* 2.7 50.3 + - + +
338A VAL* 3.9 30.1 - - + -
353A LEU* 4.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 3.2 29.5 + - - +
290A LEU* 3.6 2.8 - - - +
291A THR* 2.8 55.6 + - - +
293A TYR* 3.3 21.9 + - + -
302A LEU* 1.3 75.8 - - - +
304A CYS* 1.3 64.6 + - - +
305A GLU* 3.0 32.2 + - - +
334A ARG* 3.4 34.2 - - + +
335A TYR* 3.2 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU 3.9 3.6 - - - -
290A LEU* 3.9 4.6 - - + +
302A LEU 4.1 0.6 - - - -
303A ARG* 1.3 73.0 - - - +
305A GLU* 1.3 59.0 + - - +
306A ARG* 3.4 36.7 + - - +
309A ILE* 4.8 12.8 - - - +
311A LEU* 4.1 26.2 - - + -
334A ARG* 2.8 43.1 + - - +
336A TYR* 4.2 7.1 - - + -
356A VAL* 6.2 0.2 - - - -
357A LEU* 4.0 17.3 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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