Contacts of the helix formed by residues 2221 - 2234 (chain A) in PDB entry 1T77
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 SER2221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2215A TRP* 3.6 0.7 - - - -
2219A GLU 4.4 0.4 + - - -
2220A ILE* 1.3 81.1 - - - +
2222A ASN* 1.3 64.6 + - - +
2223A PHE 3.5 1.7 + - - -
2224A GLU* 3.1 37.5 + - - +
2225A TYR* 3.1 19.9 + - - +
2408A ARG* 3.6 14.0 + - - -
2412A GLU* 3.4 18.4 - - - -
2489A ARG* 3.8 7.2 - - - +
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Residues in contact with ASN2222 (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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2215A TRP* 2.8 26.9 + - - +
2221A SER* 1.3 70.0 - - - +
2223A PHE* 1.3 66.6 + - - +
2225A TYR* 3.3 2.1 + - - +
2226A LEU* 2.9 31.8 + - - +
2411A LEU* 3.0 31.5 + - + +
2412A GLU* 2.8 19.0 + - - +
2416A VAL* 3.9 1.8 - - - +
2417A SER* 2.9 30.7 + - - +
2420A LEU* 3.8 17.2 - - + +
2489A ARG* 3.1 18.6 + - - +
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Residues in contact with PHE2223 (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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2222A ASN* 1.3 76.9 - - - +
2224A GLU* 1.3 67.9 + - + +
2226A LEU* 3.0 5.9 + - - +
2227A MET* 2.9 51.1 + - + -
2237A TYR* 5.3 0.4 - - - -
2246A PHE* 3.5 26.5 - + - -
2362A PRO* 4.1 7.9 - - + -
2365A TYR* 4.2 10.3 - - + -
2366A TYR* 3.8 37.0 - + + -
2408A ARG* 3.5 25.4 - - - +
2411A LEU* 4.0 15.4 - - + +
2412A GLU* 3.0 19.3 + - - +
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Residues in contact with GLU2224 (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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2211A MET* 6.0 0.3 - - - +
2219A GLU 4.8 2.0 - - - +
2220A ILE* 3.4 36.1 - - + +
2221A SER* 3.1 28.5 + - - +
2223A PHE* 1.3 89.9 - - + +
2225A TYR* 1.3 61.5 + - - +
2227A MET* 3.4 6.4 + - - +
2228A PHE* 3.0 22.9 + - - +
2408A ARG* 5.6 1.1 + - - +
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Residues in contact with TYR2225 (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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2206A PHE* 3.7 8.0 - - - -
2211A MET* 4.0 6.3 - - + -
2212A THR* 3.0 37.9 + - - -
2215A TRP* 3.3 56.3 - + + -
2220A ILE* 3.6 7.1 - - + +
2221A SER 3.1 8.7 + - - +
2222A ASN 3.7 3.4 - - - +
2224A GLU* 1.3 77.0 - - - +
2226A LEU* 1.3 60.3 + - + +
2228A PHE* 3.1 27.4 - + - +
2229A LEU* 2.9 51.2 + - + +
2420A LEU* 5.4 1.1 - - + -
2424A ILE* 3.8 11.0 - - + -
2486A HIS* 2.6 32.8 + + - -
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Residues in contact with LEU2226 (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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2222A ASN 2.9 20.0 + - - +
2223A PHE 3.0 1.1 + - - +
2225A TYR* 1.3 74.6 - - + +
2227A MET* 1.3 65.8 + - - +
2229A LEU* 3.3 11.3 + - + +
2230A ASN* 2.9 30.3 + - - +
2245A VAL 5.4 0.2 - - - +
2246A PHE* 3.4 43.7 - - + -
2247A PRO* 4.0 11.0 - - + -
2411A LEU* 4.0 18.6 - - + -
2420A LEU* 4.1 25.4 - - + -
2423A TRP* 4.0 23.3 - - + -
2424A ILE* 4.5 10.8 - - + -
2428A PHE* 5.3 2.0 - - + -
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Residues in contact with MET2227 (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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2223A PHE* 2.9 38.1 + - + +
2224A GLU* 3.7 9.6 - - - +
2225A TYR 3.3 0.2 - - - -
2226A LEU* 1.3 75.7 - - - +
2228A PHE* 1.3 52.6 + - - +
2230A ASN* 3.3 4.9 + - + +
2231A THR* 2.8 47.3 + - - +
2237A TYR* 3.8 38.4 - - + -
2244A PRO* 4.3 16.2 - - + -
2246A PHE* 3.7 19.5 - - - -
2362A PRO* 4.1 8.5 - - - -
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Residues in contact with PHE2228 (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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2189A PHE* 3.9 32.8 - + + -
2206A PHE* 4.6 15.5 - + - -
2209A SER* 3.8 18.2 - - - -
2211A MET* 3.6 43.1 - - + -
2212A THR* 5.0 1.8 - - - -
2224A GLU 3.0 13.8 + - - +
2225A TYR* 3.1 26.7 - + - +
2227A MET* 1.3 74.5 - - - +
2229A LEU* 1.3 97.8 + - + +
2231A THR* 3.1 5.2 + - - -
2232A ILE* 2.9 53.5 + - + +
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Residues in contact with LEU2229 (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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2206A PHE* 3.9 9.9 - - + -
2225A TYR* 2.9 38.7 + - + +
2226A LEU* 3.3 11.2 + - + +
2228A PHE* 1.3 96.9 - - + +
2230A ASN* 1.3 57.8 + - - +
2232A ILE* 3.5 1.0 + - - -
2233A ALA* 2.9 31.6 + - - +
2424A ILE* 3.5 47.3 - - + -
2428A PHE* 3.9 15.0 - - + -
2481A LEU* 3.4 29.0 - - + +
2486A HIS* 5.0 0.2 - - - +
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Residues in contact with ASN2230 (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 LEU* 2.9 26.1 + - - +
2227A MET* 3.4 11.7 - - + +
2229A LEU* 1.3 78.2 - - - +
2231A THR* 1.3 61.0 + - - +
2233A ALA 3.2 1.0 + - - -
2234A GLY 3.2 4.3 + - - -
2235A ARG* 2.8 46.5 + - + +
2244A PRO* 3.2 16.8 - - + +
2245A VAL* 2.8 46.8 + - - +
2246A PHE* 4.0 9.7 - - - -
2428A PHE* 4.0 17.3 - - - -
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Residues in contact with THR2231 (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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2142A PHE* 3.6 33.0 - - + -
2144A ARG* 3.2 30.5 + - - +
2156A PHE* 5.0 8.0 - - + -
2189A PHE* 4.2 13.6 - - + -
2227A MET* 2.8 33.5 + - - +
2228A PHE* 3.7 6.5 - - - -
2230A ASN* 1.3 72.5 - - - +
2232A ILE* 1.3 63.0 + - - +
2234A GLY 3.1 10.0 + - - -
2235A ARG 4.0 9.6 + - - -
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Residues in contact with ILE2232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2142A PHE* 4.1 9.9 - - + -
2144A ARG* 5.1 2.6 + - - +
2145A ARG* 5.3 0.9 + - - -
2189A PHE* 3.9 26.2 - - + -
2191A LEU* 4.8 2.2 - - + -
2202A PRO* 3.3 29.7 - - - +
2205A LEU* 3.5 50.4 - - + +
2206A PHE* 4.2 5.6 - - + +
2228A PHE* 2.9 43.8 + - + +
2229A LEU* 3.9 4.3 - - - +
2231A THR* 1.3 75.8 - - - +
2233A ALA* 1.3 61.7 + - - +
2234A GLY 3.4 0.7 + - - -
2481A LEU* 3.5 11.7 - - + -
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Residues in contact with ALA2233 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2145A ARG* 4.0 3.1 + - - -
2202A PRO* 4.6 1.8 - - - -
2229A LEU 2.9 19.0 + - - +
2230A ASN 3.6 4.7 - - - +
2231A THR 3.1 0.2 - - - -
2232A ILE* 1.3 77.5 - - - +
2234A GLY* 1.3 59.1 + - - +
2235A ARG* 3.5 2.9 + - + +
2242A GLN* 5.5 1.2 - - - +
2428A PHE* 4.0 19.1 - - + -
2478A PRO* 4.3 4.1 - - + +
2479A SER* 3.3 50.6 + - - +
2481A LEU* 4.0 9.0 - - + -
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Residues in contact with GLY2234 (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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2144A ARG* 3.4 39.5 - - - -
2145A ARG* 4.3 10.9 + - - +
2231A THR 3.1 6.6 + - - -
2232A ILE 3.1 1.4 - - - -
2233A ALA* 1.3 79.6 - - - +
2235A ARG* 1.3 65.8 + - - +
2236A SER* 3.6 2.8 + - - -
2242A GLN* 4.0 20.8 + - - +
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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