Contacts of the helix formed by residues 306 - 316 (chain P) in PDB entry 1HI0
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 THR 306 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305P THR* 1.3 93.8 + - - +
307P ARG* 1.3 67.4 + - - +
308P LEU* 3.6 8.6 + - - +
309P ASN* 2.9 35.5 + - - +
310P LYS* 3.2 20.9 + - - +
499P ASP* 4.8 0.9 - - - -
617P ILE* 5.5 7.6 - - + -
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Residues in contact with ARG 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306P THR* 1.3 75.2 - - - +
308P LEU* 1.3 85.0 + - - +
310P LYS* 3.6 1.9 + - - -
311P GLU* 3.0 26.4 + - - +
499P ASP* 3.6 23.5 + - - +
514P PHE* 3.1 41.3 + - + +
515P VAL* 3.9 0.2 - - - +
516P GLY 3.9 21.1 - - - +
556P ASP 5.0 9.7 + - - -
557P THR* 4.3 12.1 - - - +
560P ALA* 3.7 25.9 - - - +
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Residues in contact with LEU 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306P THR* 3.0 7.0 + - - +
307P ARG* 1.3 117.3 - - - +
309P ASN* 1.3 65.6 + - - +
310P LYS 3.1 1.8 - - - -
311P GLU* 3.5 18.2 - - - +
312P GLU* 3.0 37.5 + - + +
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Residues in contact with ASN 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303P HIS* 3.4 11.7 + - - +
304P HIS* 3.2 19.2 + - - +
305P THR* 3.1 31.0 + - - +
306P THR* 2.9 30.7 + - - +
308P LEU* 1.3 79.1 - - - +
310P LYS* 1.3 64.3 + - - +
312P GLU* 3.7 21.4 + - - +
313P LYS* 3.8 21.5 + - - +
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Residues in contact with LYS 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P HIS* 4.2 21.8 - - + +
305P THR 4.9 7.3 + - - +
306P THR 3.2 15.7 + - - +
307P ARG* 3.7 3.1 - - - +
308P LEU 3.1 0.2 - - - -
309P ASN* 1.3 75.9 - - - +
311P GLU* 1.3 68.6 + - - +
313P LYS* 3.1 20.6 + - - +
314P VAL* 3.3 12.3 + - - +
449P ILE* 5.3 3.8 - - + +
496P PHE* 3.0 44.8 + - + +
497P LEU* 3.2 23.6 + - - +
499P ASP* 2.6 35.1 + - + +
514P PHE* 3.3 23.3 - - + -
631P LYS* 4.6 2.4 - - - +
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Residues in contact with GLU 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307P ARG* 3.0 14.6 + - - +
308P LEU* 3.5 21.7 - - + +
310P LYS* 1.3 78.3 - - - +
312P GLU* 1.3 67.7 + - + +
314P VAL* 3.3 1.4 + - - +
315P LYS* 2.9 50.7 + - + +
501P LEU* 6.4 0.2 - - + -
512P ALA 4.2 2.5 - - - +
513P ILE* 3.2 31.2 - - - +
514P PHE* 2.7 41.7 + - + +
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Residues in contact with GLU 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308P LEU* 3.0 26.8 + - + +
309P ASN* 3.8 12.3 - - - +
310P LYS 3.1 0.2 + - - -
311P GLU* 1.3 79.9 - - + +
313P LYS* 1.3 64.6 + - + +
315P LYS* 3.3 15.3 + - - +
316P GLU* 3.7 13.4 - - - +
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Residues in contact with LYS 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299P ALA* 2.8 20.0 + - - +
300P TYR* 2.8 64.9 + - + +
303P HIS 3.4 15.0 + - - -
304P HIS* 3.8 7.6 + - - +
309P ASN* 3.8 27.6 + - - +
310P LYS* 3.1 7.9 + - - +
312P GLU* 1.3 77.0 - - + +
314P VAL* 1.3 61.5 + - - +
316P GLU* 3.4 13.3 + - - +
317P TRP* 3.3 23.3 + - + -
449P ILE* 3.9 16.6 - - + -
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Residues in contact with VAL 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310P LYS 3.3 7.6 + - - +
311P GLU* 4.0 2.2 - - - +
313P LYS* 1.3 74.1 - - - +
315P LYS* 1.3 66.3 + - + +
317P TRP* 3.1 32.4 + - + +
320P CYS* 4.0 13.2 - - - -
449P ILE* 3.8 28.7 - - + -
456P MET* 4.7 0.2 - - - -
501P LEU* 3.9 30.1 - - + -
509P PRO* 3.2 23.0 - - + +
514P PHE* 3.9 20.0 - - + -
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Residues in contact with LYS 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311P GLU* 2.9 45.2 + - + +
312P GLU* 3.6 7.6 - - - +
313P LYS 3.3 0.2 - - - -
314P VAL* 1.3 77.1 - - - +
316P GLU* 1.3 60.1 + - + +
317P TRP 3.1 6.5 + - - +
509P PRO 3.3 12.3 - - - +
510P GLY* 3.3 39.8 + - - +
511P SER* 5.1 1.8 - - - +
512P ALA 2.9 25.8 + - - +
513P ILE* 4.3 6.1 - - - +
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Residues in contact with GLU 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300P TYR* 5.9 1.7 - - - -
312P GLU 3.7 14.8 - - - +
313P LYS* 3.4 10.4 + - - +
314P VAL 3.2 1.2 - - - -
315P LYS* 1.3 76.9 - - + +
317P TRP* 1.3 66.3 + - + +
318P SER* 4.2 0.7 + - - -
447P ARG* 4.2 16.3 + - - +
460P THR* 4.6 11.6 - - - +
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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