Contacts of the strand formed by residues 2219 - 2233 (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 ALA2219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2061A ILE* 3.3 14.7 - - - +
2063A GLU* 4.3 10.5 - - + +
2215A LEU* 2.9 21.3 + - + +
2216A LYS 4.2 0.7 - - - +
2217A PHE 3.4 0.9 - - - +
2218A TYR* 1.3 77.5 - - - +
2220A SER* 1.3 60.2 + - - +
2221A VAL 3.4 8.3 - - - +
2222A ARG* 3.7 29.6 - - + -
2248A LYS* 2.9 28.6 + - - -
2250A LYS* 4.1 2.1 - - - +
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Residues in contact with SER2220 (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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1098A ALA* 4.6 2.4 - - - +
2057A PRO* 4.4 9.0 - - - -
2060A ARG* 3.0 52.7 + - - +
2061A ILE 2.7 11.8 + - - -
2218A TYR 3.4 5.9 + - - -
2219A ALA* 1.3 74.1 - - - +
2221A VAL* 1.3 63.0 + - - +
2248A LYS* 4.5 2.4 - - - +
2249A ASN* 3.5 1.7 + - - -
2250A LYS* 2.8 44.2 + - - +
2251A ILE* 4.4 1.1 + - - -
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Residues in contact with VAL2221 (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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2051A LEU* 3.6 21.3 - - + -
2056A LEU* 4.1 7.6 - - + -
2057A PRO* 4.1 24.7 - - + -
2061A ILE 3.8 2.2 + - - -
2062A VAL* 3.4 16.2 - - + +
2063A GLU 3.0 23.6 + - - -
2219A ALA* 3.4 1.4 - - - +
2220A SER* 1.3 86.1 - - - +
2222A ARG* 1.3 67.9 + - - +
2223A LEU* 3.5 26.7 - - + -
2246A VAL* 4.6 0.7 - - + -
2248A LYS 3.2 8.7 - - - +
2249A ASN* 3.7 16.8 - - - +
2251A ILE* 4.8 4.0 - - + -
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Residues in contact with ARG2222 (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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1068A GLU* 4.5 8.9 + - - -
2063A GLU* 2.5 50.5 + - + +
2065A TYR* 3.7 30.6 + - + -
2209A THR* 4.5 7.9 + - - +
2216A LYS* 4.0 44.6 + - - +
2219A ALA* 3.7 20.0 - - + -
2221A VAL* 1.3 79.4 - - - +
2223A LEU* 1.3 66.8 + - - +
2246A VAL* 3.7 0.5 - - - -
2247A VAL* 2.8 41.8 + - + +
2248A LYS* 2.9 33.4 + - + +
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Residues in contact with LEU2223 (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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2047A LEU* 4.5 18.4 - - + -
2051A LEU* 4.3 3.8 - - + -
2056A LEU* 4.3 22.9 - - + -
2062A VAL* 4.6 1.6 - - + -
2063A GLU 2.7 12.0 + - - +
2064A ILE* 3.4 31.3 - - + +
2065A TYR* 2.9 35.0 + - - +
2075A LEU* 4.9 4.7 - - + -
2221A VAL* 3.5 20.0 - - + -
2222A ARG* 1.3 80.6 - - - +
2224A ASP* 1.3 59.0 + - - +
2225A ILE 3.8 0.2 - - - -
2244A VAL* 3.7 20.0 - - + -
2245A LYS 3.5 1.3 - - - +
2246A VAL* 4.0 24.9 - - + -
2247A VAL* 5.0 0.2 - - - -
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Residues in contact with ASP2224 (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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2065A TYR* 3.5 30.1 + - + +
2207A GLU* 5.0 0.7 - - - +
2222A ARG 4.2 0.4 + - - -
2223A LEU* 1.3 70.1 - - - +
2225A ILE* 1.3 62.7 + - - +
2226A ARG* 2.7 40.8 + - - +
2243A ARG 3.6 1.9 - - - +
2244A VAL* 3.3 2.7 - - - -
2245A LYS* 2.8 46.8 + - + +
2247A VAL* 3.6 23.9 - - + +
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Residues in contact with ILE2225 (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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2064A ILE* 3.8 13.9 - - + -
2065A TYR 3.0 19.2 + - - +
2066A GLY* 3.4 2.4 - - - -
2067A PRO* 3.3 15.1 - - - +
2070A SER* 3.6 24.9 - - - +
2071A GLY* 3.9 18.8 - - - +
2072A LYS* 3.6 25.8 - - + -
2075A LEU* 4.0 16.4 - - + -
2223A LEU 3.8 0.8 - - - -
2224A ASP* 1.3 72.3 - - - +
2226A ARG* 1.3 71.9 + - - +
2242A THR* 3.8 21.5 - - + -
2243A ARG 3.5 2.5 - - - -
2244A VAL* 3.8 18.8 - - + +
2260A PHE* 4.6 0.9 - - + -
2262A ILE* 4.8 2.0 - - + -
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Residues in contact with ARG2226 (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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2065A TYR* 4.6 1.6 - - - -
2067A PRO* 3.4 25.6 - - + +
2070A SER* 4.2 8.7 - - - -
2195A ILE* 3.2 19.3 - - - +
2207A GLU* 2.7 39.7 + - - -
2224A ASP* 2.7 34.4 + - - +
2225A ILE* 1.3 80.3 - - - +
2227A ARG* 1.3 67.1 + - - +
2228A ILE* 3.6 9.1 + - + +
2242A THR* 3.6 2.6 - - - +
2243A ARG* 2.9 39.4 + - + +
2245A LYS* 5.9 5.8 - - - +
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Residues in contact with ARG2227 (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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2067A PRO* 5.5 1.2 - - - +
2068A GLU 6.0 0.2 - - - +
2069A SER* 4.6 6.7 - - - +
2070A SER* 4.2 21.6 - - - +
2226A ARG* 1.3 73.9 - - - +
2228A ILE* 1.3 64.3 + - - +
2229A GLY* 3.5 26.8 + - - +
2230A ALA* 3.5 28.5 - - - +
2237A VAL* 4.1 0.8 - - - +
2239A GLY 4.0 1.6 + - - -
2240A SER* 3.0 23.9 + - - +
2241A GLU 3.6 6.5 - - - +
2242A THR* 4.7 2.9 - - - +
2264A TYR* 3.6 9.3 + - - -
2502A ADP 5.1 0.8 + - - -
3255A PHE* 3.3 38.9 - - - -
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Residues in contact with ILE2228 (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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2226A ARG* 3.9 9.2 - - + +
2227A ARG* 1.3 78.5 - - - +
2229A GLY* 1.3 58.6 + - - +
2241A GLU* 2.8 37.1 + - + +
2242A THR 4.2 4.7 - - - +
2243A ARG* 3.6 54.7 - - + +
2259A GLU* 4.0 22.0 - - + +
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Residues in contact with GLY2229 (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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2227A ARG* 3.5 23.1 - - - +
2228A ILE* 1.3 81.4 - - - +
2230A ALA* 1.3 57.1 + - - -
2240A SER* 3.7 0.2 - - - -
2241A GLU* 2.8 36.4 + - - +
2232D LYS* 5.6 5.2 - - - -
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Residues in contact with ALA2230 (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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2227A ARG* 3.5 24.4 - - - +
2229A GLY* 1.3 73.5 - - - -
2231A VAL* 1.3 63.0 + - - +
2232A LYS* 3.6 22.3 + - + +
2237A VAL* 4.0 17.9 - - + -
2239A GLY 3.7 0.2 - - - -
2241A GLU* 4.5 3.2 - - - +
2232D LYS* 4.5 15.7 + - - +
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Residues in contact with VAL2231 (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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2230A ALA* 1.3 70.1 - - - +
2232A LYS* 1.3 64.2 + - - +
2237A VAL* 3.7 2.4 - - - -
2238A VAL* 2.9 43.5 + - + +
2239A GLY* 2.8 30.0 + - - +
2240A SER 4.0 1.6 - - - -
2241A GLU* 3.4 32.1 - - - +
2261A GLN* 3.5 29.8 - - + +
2263A LEU* 4.0 13.2 - - + -
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Residues in contact with LYS2232 (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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2230A ALA* 3.6 18.1 + - + +
2231A VAL* 1.3 80.1 - - - +
2233A GLU* 1.3 62.9 + - - +
2234A GLY* 3.5 21.0 + - - +
2235A GLU 4.8 3.8 - - - +
2236A ASN 3.2 10.5 - - - +
2237A VAL* 4.2 19.1 - - + -
2238A VAL* 4.7 0.8 - - - +
2228D ILE 5.4 1.2 + - - -
2229D GLY* 4.7 17.8 - - - -
2230D ALA 4.7 11.1 + - - +
2241D GLU* 5.6 6.5 + - - +
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Residues in contact with GLU2233 (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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2231A VAL 4.2 0.2 + - - -
2232A LYS* 1.3 71.2 - - - +
2234A GLY* 1.3 53.1 + - - +
2235A GLU* 2.7 15.9 + - - +
2236A ASN* 2.7 36.2 + - + +
2238A VAL* 3.9 26.0 - - + -
2291D TYR* 4.9 3.7 + - - -
2301D GLY* 5.3 3.3 - - - -
2302D LYS* 4.1 38.9 + - - +
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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