Contacts of the helix formed by residues 2419 - 2428 (chain C) 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 GLN2419 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2268C ASP* 6.0 1.6 - - - +
2269C LEU* 4.0 20.5 - - + +
2270C SER* 5.5 0.9 - - - +
2415C PHE 4.3 7.4 - - - +
2416C VAL 3.0 2.4 + - - +
2418C CYS* 1.3 113.0 + - - +
2420C LEU* 1.3 58.8 + - - +
2421C HIS* 3.0 9.6 - - - -
2422C GLN* 2.6 68.2 + - + +
2423C TRP 3.6 2.1 + - - -
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Residues in contact with LEU2420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2215C TRP* 4.2 17.5 - - + +
2222C ASN* 3.8 37.9 - - + +
2225C TYR* 5.3 1.6 - - + -
2226C LEU* 4.3 21.8 - - + -
2247C PRO* 4.3 14.1 - - + -
2269C LEU* 4.2 8.5 - - + +
2411C LEU* 5.6 0.2 - - + -
2416C VAL* 2.8 34.6 + - + +
2417C SER* 4.1 2.1 + - - +
2419C GLN* 1.3 70.4 - - - +
2421C HIS* 1.3 63.0 + - - +
2423C TRP* 3.1 27.8 + - + +
2424C ILE* 3.0 30.3 + - + +
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Residues in contact with HIS2421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2215C TRP* 4.7 5.9 - - + -
2417C SER 4.9 0.6 + - - -
2418C CYS 3.1 26.9 + - - -
2419C GLN* 2.9 16.5 + - - -
2420C LEU* 1.3 78.6 + - - +
2422C GLN* 1.3 80.4 + - + +
2424C ILE* 3.3 14.6 + - - +
2425C ASP* 3.0 34.2 + - - +
2486C HIS* 3.3 28.3 - - + +
2487C PRO 3.4 19.7 - - - +
2488C PRO* 3.7 30.0 - - + +
2489C ARG 4.8 1.2 + - - -
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Residues in contact with GLN2422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2269C LEU 3.6 2.6 - - - +
2270C SER* 3.6 35.6 - - - +
2419C GLN* 2.6 43.2 + - + +
2421C HIS* 1.3 92.4 + - + +
2423C TRP* 1.3 63.3 + - - +
2425C ASP* 3.3 24.6 + - - +
2426C LEU* 3.4 12.6 + - - +
2431C LYS* 4.1 18.7 + - - +
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Residues in contact with TRP2423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2226C LEU* 3.7 22.4 - - + -
2245C VAL* 3.3 27.1 - - + -
2246C PHE 3.8 2.2 - - - -
2247C PRO* 3.1 55.6 - - + +
2267C ARG* 3.8 16.2 - - - -
2269C LEU* 3.1 35.7 + - + +
2359C GLU* 3.0 27.5 + - - -
2419C GLN 3.6 1.4 + - - -
2420C LEU* 3.1 13.1 + - + +
2422C GLN* 1.3 72.7 - - - +
2424C ILE* 1.3 68.9 + - - +
2426C LEU* 2.8 28.8 + - + +
2427C ILE* 3.1 39.7 + - + +
2428C PHE* 4.3 9.9 - + - -
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Residues in contact with ILE2424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2215C TRP* 5.0 1.6 - - + -
2225C TYR* 3.8 20.0 - - + -
2226C LEU* 4.9 2.0 - - + -
2229C LEU* 3.5 35.4 - - + -
2420C LEU* 3.0 28.6 + - + +
2421C HIS* 3.5 16.4 - - - +
2422C GLN 3.3 0.2 - - - -
2423C TRP* 1.3 91.0 - - + +
2425C ASP* 1.3 49.6 + - - +
2428C PHE* 2.9 25.8 + - + -
2429C GLY 2.7 28.4 + - - -
2482C LEU* 4.7 6.3 - - + -
2486C HIS* 3.6 27.1 - - + +
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Residues in contact with ASP2425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2421C HIS* 3.0 23.2 + - - +
2422C GLN* 3.4 17.6 - - - +
2423C TRP 3.1 0.4 - - - -
2424C ILE* 1.3 76.2 - - - +
2426C LEU* 1.3 59.4 + - - +
2429C GLY* 3.1 16.8 - - - -
2430C TYR* 3.4 34.7 + - + -
2431C LYS* 2.8 37.6 + - + +
2432C GLN 3.3 0.3 + - - -
2484C GLU 3.9 2.4 - - - +
2485C PRO* 3.5 1.6 - - - +
2486C HIS* 2.7 35.6 + - - +
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Residues in contact with LEU2426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2269C LEU 4.0 8.3 - - - +
2270C SER 3.2 26.7 - - - +
2271C LYS 3.5 23.8 - - - +
2272C PRO* 3.5 8.3 - - + -
2305C TYR* 4.9 1.6 + - - -
2422C GLN 3.4 7.2 + - - +
2423C TRP* 2.8 14.2 + - + +
2425C ASP* 1.3 78.7 - - - +
2427C ILE* 1.3 70.1 + - + +
2431C LYS* 4.0 12.3 - - + -
2432C GLN* 3.5 12.3 - - - +
2440C ALA* 3.9 19.7 - - + -
2442C ASN* 3.0 53.0 + - + +
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Residues in contact with ILE2427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2245C VAL* 4.7 3.4 - - + -
2272C PRO* 6.5 0.7 - - + -
2305C TYR* 3.7 48.1 + - + +
2359C GLU* 4.8 4.5 - - + +
2423C TRP* 3.1 53.2 + - + +
2426C LEU* 1.3 85.8 - - + +
2428C PHE* 1.3 90.0 + - + +
2432C GLN* 2.7 31.2 + - - +
2442C ASN* 5.4 2.2 - - - +
2478C PRO* 4.2 9.2 - - + +
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Residues in contact with PHE2428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2226C LEU* 5.0 1.3 - - + -
2229C LEU* 3.9 30.7 - - + -
2230C ASN* 3.7 36.3 - - - -
2233C ALA* 4.0 21.8 - - + -
2245C VAL* 4.7 2.5 - - + -
2423C TRP* 4.3 15.3 - + - -
2424C ILE* 2.9 18.9 + - + +
2427C ILE* 1.3 93.6 - - + +
2429C GLY* 1.3 61.4 + - - +
2432C GLN* 4.1 4.9 - - - +
2478C PRO* 3.7 31.9 - - + -
2479C SER 4.2 2.0 - - - -
2480C GLN* 3.5 10.1 - - - +
2481C LEU* 2.8 48.8 + - + +
2482C LEU* 3.7 2.9 + - - -
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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