Contacts of the helix formed by residues 2413 - 2418 (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 SER2413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2260A LEU* 5.3 6.1 - - - -
2266A PHE* 3.5 17.4 - - - -
2409A LEU 2.9 11.3 + - - -
2410A ALA* 2.6 24.4 + - - -
2412A GLU* 1.3 83.3 - - - +
2414A GLU* 1.3 63.6 + - - +
2415A PHE* 3.3 15.3 + - - -
2416A VAL* 3.2 7.4 + - - +
2417A SER* 3.1 18.9 + - - -
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Residues in contact with GLU2414 (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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2218A ARG* 3.5 36.4 + - - -
2412A GLU 5.6 0.5 - - - +
2413A SER* 1.3 72.8 - - - +
2415A PHE* 1.3 69.2 + - + +
2417A SER* 3.7 11.9 + - - -
2418A CYS* 3.0 38.9 + - + +
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Residues in contact with PHE2415 (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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2260A LEU 3.1 28.5 - - - -
2261A THR* 3.1 31.9 - - + -
2262A LEU 4.5 0.2 - - - -
2263A PRO* 3.8 34.1 - - + -
2266A PHE* 3.6 31.0 - + + -
2269A LEU* 4.7 2.1 - - - +
2413A SER* 3.1 11.4 + - - +
2414A GLU* 1.3 82.3 - - + +
2416A VAL* 1.3 60.3 + - - +
2418A CYS* 3.3 21.2 - - - -
2419A GLN* 4.0 8.7 + - - +
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Residues in contact with VAL2416 (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* 3.9 6.1 - - - +
2249A VAL* 3.4 31.4 - - + -
2266A PHE* 4.5 3.1 - - + -
2269A LEU* 4.0 17.0 - - + -
2410A ALA 3.2 21.1 - - - +
2411A LEU* 3.2 31.0 - - + +
2413A SER* 3.2 5.8 + - - +
2414A GLU 3.1 0.2 - - - -
2415A PHE* 1.3 77.4 - - - +
2417A SER* 1.3 58.5 + - - +
2418A CYS 3.2 0.2 - - - -
2419A GLN 3.0 2.4 + - - -
2420A LEU* 2.7 53.5 + - + +
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Residues in contact with SER2417 (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* 4.7 1.4 - - - -
2218A ARG* 4.4 3.0 + - - -
2222A ASN* 2.9 16.3 + - - +
2412A GLU 4.1 2.8 + - - -
2413A SER 3.1 13.8 + - - -
2414A GLU* 3.4 21.4 + - - -
2416A VAL* 1.3 79.1 - - - +
2418A CYS* 1.3 61.3 + - - +
2419A GLN 3.3 0.9 + - - -
2420A LEU* 4.0 8.0 + - - +
2421A HIS* 4.8 0.5 + - - -
2489A ARG* 2.8 64.3 + - - +
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Residues in contact with CYS2418 (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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2414A GLU* 3.0 35.5 + - + +
2415A PHE* 3.3 19.7 - - - -
2416A VAL 3.2 0.2 + - - -
2417A SER* 1.3 77.5 - - - +
2419A GLN* 1.3 86.3 + - - +
2421A HIS* 3.2 13.7 - - - -
2488A PRO* 5.0 3.8 - - - +
2489A ARG 5.7 0.9 - - - +
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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