Contacts of the strand formed by residues 2236 - 2249 (chain A) in PDB entry 3CMT
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 ASN2236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2232A LYS* 3.2 6.1 - - - +
2233A GLU* 2.7 50.6 + - + +
2235A GLU* 1.3 86.5 - - - +
2237A VAL* 1.3 65.0 + - - +
2238A VAL* 3.6 4.0 + - + +
3256A LYS* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227A ARG* 4.1 1.3 - - - +
2230A ALA* 4.0 17.5 - - + -
2231A VAL 3.7 3.4 - - - +
2232A LYS* 4.2 17.3 - - + -
2235A GLU 3.9 3.8 + - - +
2236A ASN* 1.3 74.9 - - - +
2238A VAL* 1.3 61.3 + - - +
2239A GLY 3.9 17.3 - - - +
2264A TYR* 3.7 12.6 - - + -
3253A ALA* 5.4 2.3 - - - +
3254A PRO 4.2 7.2 - - - +
3255A PHE* 3.6 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2231A VAL* 2.9 32.6 + - + +
2232A LYS 4.7 0.4 - - - -
2233A GLU* 3.9 30.7 - - + -
2236A ASN* 3.6 4.9 + - + -
2237A VAL* 1.3 72.3 - - - +
2239A GLY* 1.3 56.4 + - - +
2263A LEU* 3.8 12.4 - - + +
2264A TYR* 3.1 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227A ARG* 4.0 0.2 + - - -
2230A ALA* 3.7 4.7 - - - -
2231A VAL* 2.8 39.1 + - - +
2237A VAL* 3.9 3.5 - - - +
2238A VAL* 1.3 81.5 - - - +
2240A SER* 1.3 56.7 + - - -
2262A ILE 3.1 13.5 - - - -
2263A LEU* 4.1 2.5 - - - -
2264A TYR* 3.5 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2069A SER 4.9 1.4 + - - -
2070A SER 5.7 1.8 - - - -
2227A ARG* 3.0 27.9 + - - +
2229A GLY 3.7 4.3 - - - -
2231A VAL* 4.0 2.7 - - - +
2239A GLY* 1.3 72.7 - - - -
2241A GLU* 1.3 61.6 - - - +
2242A THR* 3.3 10.4 + - - -
2261A GLN* 3.6 0.9 - - - -
2262A ILE* 2.7 46.1 + - - -
2264A TYR* 2.7 25.7 + - - -
2502A ADP 3.5 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227A ARG* 3.6 4.0 - - - -
2228A ILE* 2.8 43.6 + - + -
2229A GLY* 2.8 31.9 + - - +
2230A ALA 4.4 3.1 - - - +
2231A VAL* 3.4 13.1 - - + +
2240A SER* 1.3 71.6 - - - +
2242A THR* 1.3 59.4 + - - +
2259A GLU* 5.6 3.1 - - + +
2260A PHE* 3.7 10.4 + - - +
2261A GLN* 3.2 39.7 + - - +
2232D LYS* 5.1 10.3 + - - +
2234D GLY* 5.2 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2070A SER 4.2 5.8 + - - +
2225A ILE* 3.8 28.7 - - + -
2226A ARG 3.6 6.2 + - - +
2227A ARG* 4.8 0.9 - - - -
2228A ILE* 4.4 3.8 - - - +
2240A SER* 3.3 17.7 + - - -
2241A GLU* 1.3 74.3 + - - +
2243A ARG* 1.3 64.5 + - - +
2258A ALA 4.5 0.2 - - - -
2259A GLU* 3.2 7.6 - - - +
2260A PHE* 2.7 72.5 + - + -
2262A ILE* 3.7 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2224A ASP 3.6 1.9 - - - +
2225A ILE* 3.5 1.2 - - - -
2226A ARG* 2.9 39.5 + - + +
2228A ILE* 3.6 39.2 - - + +
2242A THR* 1.3 76.0 - - - +
2244A VAL* 1.3 65.7 + - - +
2245A LYS* 4.1 22.9 - - - +
2257A GLN* 3.3 30.4 + - - +
2258A ALA 3.3 5.2 - - - +
2259A GLU* 2.4 43.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2047A LEU* 4.3 19.7 - - + +
2075A LEU* 4.3 6.7 - - + -
2223A LEU* 3.7 36.1 - - + -
2224A ASP 3.3 7.0 - - - +
2225A ILE* 3.8 24.9 - - + -
2243A ARG* 1.3 77.2 - - - +
2245A LYS* 1.3 66.6 + - - +
2246A VAL* 5.2 1.2 - - - +
2257A GLN* 3.2 4.8 - - - +
2258A ALA* 2.8 38.0 + - + +
2260A PHE* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2223A LEU* 3.5 4.2 - - - -
2224A ASP* 2.8 50.8 + - + +
2226A ARG* 5.9 5.7 - - - +
2243A ARG* 4.1 19.2 - - - +
2244A VAL* 1.3 75.0 - - - +
2246A VAL* 1.3 61.9 + - - +
2247A VAL* 3.3 13.6 + - + +
2255A PHE* 6.1 5.8 - - + +
2256A LYS 4.0 3.4 - - - +
2257A GLN* 3.4 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2047A LEU* 4.3 9.4 - - + -
2050A ALA* 4.1 28.7 - - + +
2051A LEU* 4.4 6.5 - - + -
2221A VAL* 4.6 0.2 - - + -
2222A ARG 3.7 4.9 - - - +
2223A LEU* 4.0 17.3 - - + -
2244A VAL 5.2 0.9 - - - +
2245A LYS* 1.3 71.9 - - - +
2247A VAL* 1.3 59.8 + - - +
2248A LYS 3.6 20.0 - - - +
2249A ASN* 4.0 26.0 - - + +
2254A PRO* 4.2 2.9 - - + +
2255A PHE* 2.8 37.3 + - - +
2256A LYS 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069A SER* 6.1 0.5 - - - -
2065A TYR* 3.5 26.9 - - + +
2222A ARG* 2.8 30.2 + - + +
2224A ASP* 3.6 24.9 - - + +
2245A LYS* 3.9 12.8 - - + +
2246A VAL* 1.3 74.3 - - - +
2248A LYS* 1.3 60.2 + - + +
2254A PRO* 4.6 1.7 - - - +
2255A PHE* 3.5 31.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068A GLU* 3.8 9.3 - - + +
1069A SER* 3.3 23.3 - - - +
1501A ALF 2.9 32.2 - - - -
2216A LYS 2.7 29.2 + - - +
2217A PHE 2.8 23.6 + - - -
2219A ALA 2.9 20.8 + - - +
2220A SER 4.8 0.4 - - - +
2221A VAL* 3.2 5.0 - - - -
2222A ARG* 2.9 47.9 + - + +
2246A VAL* 3.6 9.0 - - - +
2247A VAL* 1.3 79.9 - - + +
2249A ASN* 1.3 67.9 + - - +
2250A LYS* 4.5 6.3 - - - -
2254A PRO* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069A SER* 4.7 1.6 + - - -
1502A ADP 3.4 24.3 + - - -
2051A LEU* 3.2 28.3 + - - +
2220A SER 3.5 2.2 - - - -
2221A VAL* 3.7 9.7 - - - +
2246A VAL* 4.0 12.5 - - + +
2248A LYS* 1.3 81.8 - - - +
2250A LYS* 1.3 60.4 + - - +
2251A ILE* 3.0 29.5 + - - +
2252A ALA* 3.0 33.2 + - - +
2253A ALA 3.3 12.1 + - - -
2254A PRO* 3.8 19.1 - - + +
----------------------------------------------------------
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