Contacts of the helix formed by residues 2221 - 2234 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2215D TRP* 4.1 0.7 - - - -
2219D GLU 4.3 0.4 - - - -
2220D ILE* 1.3 76.9 - - - +
2222D ASN* 1.3 59.4 + - - +
2223D PHE 3.5 0.2 + - - -
2224D GLU* 3.0 36.0 + - - +
2225D TYR* 2.9 26.9 + - - +
2408D ARG* 3.1 29.8 + - - -
2412D GLU* 3.6 7.9 - - - -
2489D ARG* 3.8 7.0 - - - +
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Residues in contact with ASN2222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2215D TRP* 2.6 39.8 + - - +
2221D SER* 1.3 71.6 - - - +
2223D PHE* 1.3 62.9 + - - +
2225D TYR* 3.2 1.8 + - - +
2226D LEU* 2.8 30.6 + - - +
2411D LEU* 3.1 31.2 + - + +
2412D GLU* 3.0 20.4 + - - +
2416D VAL* 4.0 7.3 - - - +
2417D SER* 3.1 23.0 + - - +
2420D LEU* 4.1 14.8 - - + -
2489D ARG* 3.2 15.7 + - - +
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Residues in contact with PHE2223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2222D ASN* 1.3 77.3 - - - +
2224D GLU* 1.3 67.9 + - + +
2226D LEU* 3.2 3.1 + - - +
2227D MET* 3.0 49.1 + - + +
2246D PHE* 3.3 32.5 - + - -
2362D PRO* 3.9 17.3 - - + -
2365D TYR* 4.1 10.5 - - + -
2366D TYR* 3.8 27.6 - + + -
2408D ARG* 3.4 23.3 - - - +
2411D LEU* 4.0 15.8 - - + +
2412D GLU* 3.0 18.3 + - - +
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Residues in contact with GLU2224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2219D GLU 4.5 2.9 - - - +
2220D ILE* 3.4 31.3 - - + +
2221D SER* 3.0 33.7 + - - +
2223D PHE* 1.3 85.7 - - + +
2225D TYR* 1.3 61.8 + - - +
2227D MET* 3.2 7.1 + - - +
2228D PHE* 2.9 27.5 + - - +
2408D ARG* 5.1 0.8 + - - +
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Residues in contact with TYR2225 (chain D).
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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2206D PHE* 3.4 8.3 - - - -
2211D MET* 3.9 6.5 - - + -
2212D THR* 2.7 46.7 + - - -
2215D TRP* 3.5 56.3 - + + -
2220D ILE* 3.5 7.9 - - + +
2221D SER 2.9 8.6 + - - +
2222D ASN 3.7 2.7 - - - +
2224D GLU* 1.3 72.5 - - - +
2226D LEU* 1.3 67.9 + - - +
2228D PHE* 3.1 25.7 + + - +
2229D LEU* 2.8 45.9 + - + +
2420D LEU* 5.0 3.1 - - + -
2424D ILE* 3.9 8.3 - - + -
2486D HIS* 2.8 29.6 + - - -
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Residues in contact with LEU2226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2222D ASN 2.8 25.0 + - - +
2223D PHE 3.4 4.3 - - - +
2225D TYR* 1.3 72.9 - - + +
2227D MET* 1.3 57.5 + - - +
2229D LEU* 3.1 10.6 + - + +
2230D ASN* 2.9 36.0 + - - +
2245D VAL 5.5 0.7 - - - +
2246D PHE* 3.6 38.6 - - + -
2247D PRO* 3.9 14.4 - - + -
2411D LEU* 3.9 17.5 - - + -
2420D LEU* 3.8 26.9 - - + -
2423D TRP* 3.9 27.4 - - + -
2424D ILE* 4.6 8.1 - - + -
2428D PHE* 5.7 0.4 - - + -
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Residues in contact with MET2227 (chain D).
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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2223D PHE* 3.0 38.9 + - + +
2224D GLU* 3.5 10.5 - - - +
2226D LEU* 1.3 76.5 - - - +
2228D PHE* 1.3 57.1 + - - +
2230D ASN* 3.3 4.5 + - + +
2231D THR* 2.8 43.2 + - - +
2237D TYR* 3.5 37.0 - - + +
2244D PRO* 4.8 11.7 - - + -
2246D PHE* 3.6 22.4 - - + -
2362D PRO* 4.1 9.0 - - - -
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Residues in contact with PHE2228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189D PHE* 3.5 43.1 - + + -
2191D LEU* 5.8 0.2 - - + -
2205D LEU 4.6 2.9 - - - -
2206D PHE* 4.5 12.6 - + - -
2209D SER* 3.5 26.0 - - - -
2211D MET* 3.6 31.6 - - + -
2212D THR* 5.1 1.1 - - - -
2220D ILE* 6.1 0.4 - - + -
2224D GLU 2.9 13.8 + - - +
2225D TYR* 3.3 25.6 - + + +
2227D MET* 1.3 78.0 - - - +
2229D LEU* 1.3 78.2 + - + +
2231D THR* 3.2 5.3 + - - -
2232D ILE* 2.9 52.5 + - + +
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Residues in contact with LEU2229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2206D PHE* 3.9 13.5 - - + -
2225D TYR* 2.8 46.9 + - + +
2226D LEU* 3.5 11.9 - - + +
2228D PHE* 1.3 84.4 - - + +
2230D ASN* 1.3 57.7 + - - +
2232D ILE 3.4 0.2 + - - -
2233D ALA* 2.9 30.8 + - - +
2424D ILE* 3.5 49.4 - - + -
2428D PHE* 3.9 16.2 - - + -
2481D LEU* 3.5 28.4 - - + +
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Residues in contact with ASN2230 (chain D).
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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2226D LEU* 2.9 26.4 + - - +
2227D MET* 3.6 10.1 - - + +
2229D LEU* 1.3 76.5 - - - +
2231D THR* 1.3 64.2 + - - +
2233D ALA* 3.1 6.4 + - - +
2235D ARG* 3.0 43.2 + - + +
2244D PRO* 3.1 17.0 - - + +
2245D VAL* 2.7 48.0 + - - +
2246D PHE* 4.2 7.5 - - - -
2428D PHE* 3.9 19.3 - - - -
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Residues in contact with THR2231 (chain D).
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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2142D PHE* 3.6 31.9 - - + -
2144D ARG* 3.0 30.3 + - - +
2156D PHE* 5.4 6.5 - - + -
2189D PHE* 4.2 14.1 - - + -
2227D MET* 2.8 33.3 + - - +
2228D PHE* 3.2 7.3 + - - -
2230D ASN* 1.3 74.6 - - - +
2232D ILE* 1.3 60.5 + - - +
2234D GLY* 3.2 8.1 + - - -
2235D ARG 4.0 10.1 + - - -
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Residues in contact with ILE2232 (chain D).
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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2142D PHE* 4.4 12.3 - - + -
2144D ARG* 5.1 1.7 + - - +
2145D ARG* 4.9 1.6 + - - -
2185D VAL* 4.9 0.9 - - + -
2189D PHE* 4.4 15.0 - - + -
2191D LEU* 5.0 2.0 - - + -
2202D PRO* 3.5 22.0 - - - +
2205D LEU* 3.3 52.6 - - + +
2206D PHE* 4.2 7.9 - - - +
2228D PHE* 2.9 47.2 + - + +
2229D LEU* 3.9 3.6 - - - +
2231D THR* 1.3 75.0 - - - +
2233D ALA* 1.3 59.5 + - - +
2234D GLY 3.2 1.2 + - - -
2481D LEU* 3.7 19.3 - - + -
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Residues in contact with ALA2233 (chain D).
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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2145D ARG* 4.3 2.5 + - - -
2229D LEU 2.9 17.4 + - - +
2230D ASN 3.1 5.3 + - - +
2232D ILE* 1.3 76.4 - - - +
2234D GLY* 1.3 59.4 + - - +
2235D ARG* 3.5 2.3 + - + +
2242D GLN* 5.6 0.2 - - - +
2428D PHE* 3.4 30.3 - - + -
2478D PRO* 4.3 5.3 - - + +
2479D SER* 3.0 41.2 + - - +
2481D LEU* 3.6 11.9 - - + -
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Residues in contact with GLY2234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2144D ARG* 3.4 37.9 - - - -
2145D ARG* 4.0 12.7 + - - -
2231D THR 3.2 6.1 + - - -
2232D ILE 3.2 1.8 + - - -
2233D ALA* 1.3 80.2 - - - +
2235D ARG* 1.3 66.3 + - - +
2236D SER* 3.6 2.6 + - - -
2242D GLN* 3.7 20.6 - - - +
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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