Contacts of the helix formed by residues 323 - 337 (chain C) in PDB entry 1D1T
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 LYS 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU* 5.4 0.4 - - - -
96C GLN* 3.3 26.3 - - + +
102C ALA 3.4 3.2 + - - -
103C CYS* 2.9 31.8 + - - +
105C ASN 3.1 14.5 + - - -
106C PRO* 3.8 20.0 - - - +
108C GLY 2.7 31.1 + - - +
109C ASN* 4.2 9.1 - - + +
321C GLY 3.9 2.4 + - - +
322C LEU* 1.3 73.9 - - - +
324C SER* 1.3 52.0 + - - +
326C ASP* 2.7 43.0 + - + +
327C ASP* 3.0 20.2 + - - +
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Residues in contact with SER 324 (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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92C LEU* 3.4 20.5 - - - +
94C LEU* 2.8 31.2 + - - +
95C PRO 3.3 20.2 + - - -
96C GLN* 3.4 2.8 - - - +
319C PHE* 4.0 20.6 - - - -
322C LEU* 3.4 6.0 + - - -
323C LYS* 1.3 70.1 - - - +
325C ARG* 1.3 68.8 + - - -
328C VAL* 3.0 31.2 + - - +
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Residues in contact with ARG 325 (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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82C THR* 3.7 31.3 + - - +
92C LEU* 3.5 20.9 - - + -
96C GLN* 2.9 43.5 + - + +
97C CYS* 4.2 7.5 + - - +
98C ARG* 3.9 36.0 + - - +
154C GLU* 3.9 16.1 + - - +
155C SER* 3.9 22.4 + - - +
157C VAL 3.3 18.8 - - - +
158C ALA* 4.8 4.0 - - - +
324C SER* 1.3 79.6 + - - +
326C ASP* 1.3 58.9 + - - +
329C PRO* 3.2 22.3 - - - +
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Residues in contact with ASP 326 (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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96C GLN* 3.1 25.0 + - - -
98C ARG* 3.0 22.8 + - - -
323C LYS* 2.7 26.8 + - + +
325C ARG* 1.3 71.2 - - - +
327C ASP* 1.3 73.1 + - - +
329C PRO* 3.4 14.9 - - - +
330C LYS* 3.4 28.7 + - - +
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Residues in contact with ASP 327 (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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185C LYS* 3.5 18.1 - - - -
321C GLY 4.8 0.2 - - - +
322C LEU* 3.3 37.4 - - + +
323C LYS* 3.0 30.0 + - - +
326C ASP* 1.3 84.2 - - - +
328C VAL* 1.3 60.9 + - - +
330C LYS* 3.1 19.3 + - - +
331C LEU* 2.8 33.3 + - + +
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Residues in contact with VAL 328 (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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90C ILE* 4.3 12.8 - - + -
92C LEU* 4.1 8.1 - - + -
158C ALA* 3.9 20.2 - - + -
160C ILE* 4.3 10.8 - - + -
172C ILE* 3.8 23.1 - - + +
319C PHE* 3.6 36.3 - - + -
322C LEU* 4.8 4.0 - - + -
324C SER* 3.0 23.5 + - - +
327C ASP* 1.3 76.2 - - - +
329C PRO* 1.3 66.6 - - + +
331C LEU* 3.2 4.6 + - - +
332C VAL* 3.2 20.8 + - - +
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Residues in contact with PRO 329 (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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158C ALA* 4.5 8.1 - - + -
159C LYS 3.4 22.9 - - - +
160C ILE* 4.2 14.0 - - + -
161C ASP* 5.6 0.5 + - - +
324C SER 3.9 0.9 - - - +
325C ARG 3.2 25.6 - - - +
326C ASP 3.4 10.8 - - - +
328C VAL* 1.3 94.1 - - + +
330C LYS* 1.3 60.6 + - + +
332C VAL* 3.2 5.9 + - + +
333C THR* 3.1 23.9 + - - -
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Residues in contact with LYS 330 (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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326C ASP* 3.4 29.4 + - - +
327C ASP* 3.1 20.5 + - - +
328C VAL 3.1 0.2 - - - -
329C PRO* 1.3 79.5 - - + +
331C LEU* 1.3 57.2 + - + +
333C THR* 2.9 12.4 + - - -
334C GLU* 2.9 40.7 + - - +
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Residues in contact with LEU 331 (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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172C ILE* 3.5 15.6 - - + +
176C PHE* 4.0 13.0 - - + -
177C SER* 3.4 21.5 - - - +
180C TYR* 4.2 17.3 - - + -
322C LEU* 3.3 37.0 - - + -
327C ASP* 2.8 20.8 + - + +
328C VAL* 3.7 4.7 - - - +
330C LYS* 1.3 72.4 - - + +
332C VAL* 1.3 60.1 + - - +
334C GLU* 3.8 13.5 - - - +
335C PHE 3.3 2.1 + - - -
340C PHE* 2.8 55.8 - - + -
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Residues in contact with VAL 332 (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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90C ILE* 4.4 6.5 - - + -
160C ILE* 3.6 36.8 - - + -
161C ASP* 4.1 13.7 - - + +
164C ALA* 3.7 29.6 - - + -
169C VAL* 4.6 4.3 - - + -
172C ILE* 3.5 20.4 - - + -
328C VAL 3.2 14.7 + - - +
329C PRO 3.3 8.1 - - - +
330C LYS 3.1 0.4 - - - -
331C LEU* 1.3 73.8 - - - +
333C THR* 1.3 68.1 + - - +
335C PHE* 3.0 14.8 + - - +
336C LEU* 3.0 14.3 + - + +
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Residues in contact with THR 333 (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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161C ASP* 5.2 7.0 - - - +
329C PRO 3.1 11.7 + - - -
330C LYS* 2.9 12.0 + - - -
332C VAL* 1.3 80.6 - - - +
334C GLU* 1.3 62.4 + - + +
336C LEU* 3.1 13.1 + - + +
337C ALA* 3.0 25.0 + - + +
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Residues in contact with GLU 334 (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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180C TYR* 4.3 10.7 + - - -
330C LYS* 2.9 27.5 + - - +
331C LEU* 4.1 12.4 + - - +
332C VAL 3.2 0.2 - - - -
333C THR* 1.3 77.0 - - + +
335C PHE* 1.3 58.1 + - - +
337C ALA* 3.6 2.9 + - - -
339C LYS* 2.9 59.3 + - + +
340C PHE* 3.3 29.8 - - + -
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Residues in contact with PHE 335 (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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165C PRO* 3.9 23.6 - - + -
168C LYS* 3.7 25.6 - - + -
169C VAL* 4.2 15.7 - - + -
172C ILE* 4.9 0.7 - - + -
331C LEU 3.3 6.2 + - - +
332C VAL* 3.0 12.4 + - - +
334C GLU* 1.3 73.9 - - - +
336C LEU* 1.3 68.7 + - + +
337C ALA 3.1 1.6 - - - -
338C LYS* 2.8 24.3 + - - +
340C PHE* 3.2 49.3 - + + -
341C ASP* 4.5 1.3 - - - -
342C LEU* 3.4 43.7 - - + -
343C ASP* 4.7 3.1 - - - -
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Residues in contact with LEU 336 (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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161C ASP* 3.2 42.2 - - + +
163C ALA* 3.8 27.1 - - + +
164C ALA* 4.0 11.0 - - + +
165C PRO* 4.3 8.5 - - + -
332C VAL* 3.0 18.8 + - + +
333C THR* 3.1 13.7 + - + +
335C PHE* 1.3 81.7 - - + +
337C ALA* 1.3 57.4 + - - +
338C LYS* 3.0 13.5 + - - +
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Residues in contact with ALA 337 (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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333C THR* 3.0 16.1 + - + +
334C GLU 4.0 2.0 - - - +
335C PHE 3.1 0.6 - - - -
336C LEU* 1.3 74.8 - - - +
338C LYS* 1.3 62.9 + - - +
339C LYS* 2.8 44.5 + - - +
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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