Contacts of the helix formed by residues 300 - 315 (chain I) in PDB entry 4DVQ
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 SER 300 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D GLN* 3.9 27.2 + - - -
74D GLU* 3.9 20.6 + - - -
126I LYS* 3.8 9.9 + - - -
139I PHE* 5.9 0.4 - - - -
299I LEU* 1.3 74.4 - - - +
301I LEU* 1.3 66.5 + - - +
302I GLU* 4.0 6.5 - - - +
303I ALA* 2.9 33.0 + - - +
304I ILE* 2.8 21.9 + - - +
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Residues in contact with LEU 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271I ILE* 5.5 2.9 - - + -
275I TYR* 3.7 50.7 - - + +
294I LEU* 4.2 12.1 - - + -
299I LEU 3.8 0.8 + - - -
300I SER* 1.3 71.0 - - - +
302I GLU* 1.3 71.2 + - + +
304I ILE* 2.9 11.3 + - + +
305I LYS* 2.8 56.2 + - + +
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Residues in contact with GLU 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D GLU* 5.4 3.4 - - - +
124I GLY 5.1 5.2 - - - +
125I HIS* 5.0 9.5 + - - +
126I LYS* 4.1 28.9 + - + +
300I SER* 3.1 6.1 - - - +
301I LEU* 1.3 86.1 - - + +
303I ALA* 1.3 57.1 + - - +
305I LYS* 3.4 30.9 + - - +
306I ALA* 3.1 25.6 + - - +
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Residues in contact with ALA 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I LYS* 3.8 20.8 - - + +
127I CYS 5.7 0.9 - - - +
139I PHE* 6.0 0.9 - - + -
140I ASN* 4.1 17.0 - - - +
299I LEU* 4.2 11.9 - - + -
300I SER* 2.9 29.7 + - - +
302I GLU* 1.3 73.9 - - - +
304I ILE* 1.3 63.8 + - - +
306I ALA* 3.5 6.6 + - - +
307I ASN* 2.7 33.2 + - - -
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Residues in contact with ILE 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271I ILE* 6.3 2.2 - - + -
290I VAL* 4.6 12.1 - - + -
293I LEU* 3.5 45.3 - - + +
294I LEU* 3.7 37.2 - - + -
297I ALA* 4.9 2.7 - - - -
299I LEU* 3.2 38.1 - - + +
300I SER 2.8 13.9 + - - +
301I LEU* 3.4 8.5 - - + +
303I ALA* 1.3 75.4 - - - +
305I LYS* 1.3 61.2 + - + +
307I ASN* 3.4 3.7 + - - +
308I SER* 2.8 30.1 + - - -
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Residues in contact with LYS 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268I ASP* 4.6 15.0 + - - +
271I ILE* 3.9 37.3 - - + +
272I GLN* 6.1 4.5 - - - +
275I TYR* 6.4 0.7 - - - -
301I LEU* 2.8 43.4 + - + +
302I GLU* 3.5 33.8 + - - +
304I ILE* 1.3 76.3 - - - +
306I ALA* 1.3 62.6 + - - +
308I SER* 3.8 1.1 - - - -
309I MET* 3.0 30.5 + - + +
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Residues in contact with ALA 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I ARG* 5.8 2.1 + - - +
125I HIS* 5.9 1.1 - - + -
126I LYS* 3.3 30.1 - - + +
127I CYS 3.8 19.5 - - - +
128I GLY* 3.8 1.1 - - - +
264I PHE* 6.4 1.1 - - - -
302I GLU 3.1 16.3 + - - +
303I ALA* 3.8 7.0 - - - +
304I ILE 3.2 0.2 - - - -
305I LYS* 1.3 79.1 - - - +
307I ASN* 1.3 59.8 + - - +
309I MET* 3.6 6.2 + - - +
310I GLU* 3.0 26.5 + - - +
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Residues in contact with ASN 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I GLY* 3.9 3.3 - - - -
129I VAL* 2.8 32.4 + - - +
140I ASN* 3.3 22.0 + - - +
144I LEU* 3.4 38.4 - - + +
293I LEU* 5.5 2.0 - - + -
299I LEU* 4.4 7.7 - - - +
303I ALA 2.7 26.2 + - - +
304I ILE* 4.1 3.4 - - - +
306I ALA* 1.3 74.1 - - - +
308I SER* 1.3 61.0 + - - +
310I GLU* 3.2 7.6 + - - +
311I LEU* 2.9 37.6 + - + +
451I LEU* 5.7 0.6 - - + +
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Residues in contact with SER 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204I LEU* 6.0 0.2 - - - +
205I PHE* 3.4 31.5 - - - -
271I ILE* 3.7 16.3 - - - +
290I VAL* 3.9 17.0 - - - +
293I LEU* 6.0 1.9 - - - +
304I ILE* 2.8 21.0 + - - -
305I LYS 3.8 4.0 - - - -
307I ASN* 1.3 73.2 - - - +
309I MET* 1.3 55.6 + - - +
311I LEU* 3.0 11.0 + - - +
312I THR* 2.7 38.7 + - - -
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Residues in contact with MET 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I ARG* 5.8 2.2 - - - +
260I TRP* 4.6 1.1 - - + -
263I ILE* 3.4 33.9 - - + +
264I PHE* 3.5 66.6 - - + +
267I GLY* 3.8 19.1 - - - -
268I ASP* 4.1 2.7 - - + -
271I ILE* 4.4 8.4 - - + +
305I LYS 3.0 20.9 + - - +
306I ALA* 3.7 6.3 - - - +
308I SER* 1.3 74.1 - - - +
310I GLU* 1.3 58.8 + - + +
312I THR* 4.5 3.8 - - + -
313I ALA* 2.7 38.5 + - + +
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Residues in contact with GLU 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I TRP* 6.3 0.4 - - - -
120I ARG* 4.5 11.8 + - - +
128I GLY* 3.0 33.4 + - - +
129I VAL* 3.4 4.7 + - - +
130I PHE* 2.8 38.0 + - - +
131I LEU* 4.1 16.2 + - - +
306I ALA 3.0 16.8 - - - +
307I ASN* 3.2 10.1 + - - +
308I SER 3.2 0.6 - - - -
309I MET* 1.3 77.3 - - + +
311I LEU* 1.3 59.4 + - - +
313I ALA* 4.6 0.2 - - - -
314I GLY* 2.9 26.7 + - - -
601I HEM 4.8 6.9 - - + +
602I 1CA 3.1 30.8 - - + +
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Residues in contact with LEU 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I LEU* 5.1 0.7 - - + -
148I VAL* 4.2 27.4 - - + -
204I LEU* 3.8 30.8 - - + +
289I ILE* 4.8 3.1 - - + -
290I VAL* 5.1 1.6 - - + -
293I LEU* 4.9 10.5 - - + -
307I ASN* 2.9 28.5 + - + +
308I SER* 3.5 6.7 - - - +
310I GLU* 1.3 75.7 - - + +
312I THR* 1.3 61.5 + - - +
315I SER* 2.9 31.7 + - - -
451I LEU* 4.0 24.9 - - + -
601I HEM 3.8 35.6 - - + +
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Residues in contact with THR 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201I ASN* 5.3 2.0 - - - +
204I LEU* 3.9 5.9 - - + +
205I PHE* 3.5 31.7 - - + -
223I PHE* 4.0 6.8 - - + -
263I ILE* 6.5 0.2 - - + -
266I TYR* 3.9 33.2 - - + -
267I GLY* 4.4 13.2 - - - -
270I CYS* 4.9 0.2 - - - -
308I SER* 2.7 23.4 + - - -
309I MET* 3.8 6.9 - - + -
311I LEU* 1.3 72.7 - - - +
313I ALA* 1.3 64.3 + - - +
315I SER* 3.0 17.5 + - - -
316I VAL* 3.8 12.0 - - - +
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Residues in contact with ALA 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I PHE* 4.4 10.3 - - - -
227I LEU* 3.6 25.5 - - + +
230I MET* 6.2 0.7 - - + -
231I PHE* 5.3 1.4 - - - -
260I TRP* 4.7 10.8 - - + -
263I ILE* 4.1 23.6 - - + -
309I MET* 2.7 25.2 + - + +
310I GLU 4.1 1.6 - - - +
312I THR* 1.3 75.7 - - - +
314I GLY* 1.3 61.3 + - - +
315I SER 3.5 0.7 + - - -
316I VAL* 4.2 5.0 + - - +
317I ASP* 4.7 2.1 + - - +
602I 1CA 4.5 12.8 - - + +
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Residues in contact with GLY 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I GLU 2.9 19.4 + - - -
311I LEU 4.0 0.9 - - - -
312I THR 3.2 0.2 - - - -
313I ALA* 1.3 76.8 - - - +
315I SER* 1.3 52.9 + - - +
316I VAL 3.4 2.2 + - - -
317I ASP 5.3 0.2 - - - -
318I THR* 2.6 37.4 + - - +
601I HEM 3.7 11.1 - - - -
602I 1CA 3.8 28.0 - - - +
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Residues in contact with SER 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I THR* 4.0 6.6 - - - +
200I SER* 3.1 38.8 + - - -
204I LEU* 4.3 2.3 - - - +
311I LEU 2.9 21.5 + - - -
312I THR* 3.0 12.6 + - - -
313I ALA 3.3 0.4 - - - -
314I GLY* 1.3 77.8 - - - +
316I VAL* 1.3 60.4 + - - +
318I THR* 3.9 3.6 - - - -
319I THR* 3.5 13.0 + - - -
455I LEU* 4.9 1.3 - - - -
459I GLU* 4.3 0.2 - - - +
601I HEM 3.4 26.5 - - - -
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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