Contacts of the strand formed by residues 307 - 320 (chain A) in PDB entry 1H6T
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 ALA 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A LEU* 3.2 28.9 + - + +
233A ASP 3.7 17.3 - - - +
235A LEU* 4.1 21.5 - - + +
302A VAL* 3.7 0.7 - - - +
303A THR* 3.3 7.9 - - - +
304A ILE 3.0 37.4 + - - +
306A LYS* 1.3 78.8 - - - +
308A LYS* 1.3 59.4 + - - +
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Residues in contact with LYS 308 (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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233A ASP 4.8 1.4 + - - -
235A LEU 4.0 8.3 + - - +
299A TYR* 4.8 5.1 + - - -
301A PRO* 3.8 28.7 - - - +
302A VAL 3.3 11.7 - - - +
303A THR* 4.4 11.4 - - + +
306A LYS 3.6 3.8 + - - +
307A ALA* 1.3 73.1 - - - +
309A ALA* 1.3 80.3 + - - +
310A ARG* 6.3 0.7 - - + -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 3.1 50.7 - - + +
237A LEU* 4.4 7.2 - - + +
301A PRO* 3.7 4.2 - - - +
302A VAL* 2.8 44.5 + - + +
308A LYS* 1.3 82.3 - - - +
310A ARG* 1.3 65.2 + - - +
311A PHE 3.6 0.5 + - - -
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Residues in contact with ARG 310 (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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235A LEU 5.0 0.6 + - - -
236A GLU* 6.0 0.2 - - - +
237A LEU* 3.2 29.9 + - - +
238A PHE* 3.3 39.6 + - + +
239A SER* 5.6 0.6 + - - -
299A TYR* 3.7 32.1 - - + +
308A LYS* 6.3 0.7 - - + -
309A ALA* 1.3 71.5 - - - +
311A PHE* 1.3 59.6 - - - +
312A HIS* 3.3 40.4 + - + +
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Residues in contact with PHE 311 (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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220A ILE* 3.5 26.0 - - + -
221A SER 3.9 13.7 - - - -
223A LEU* 3.4 44.9 - - + -
237A LEU* 3.7 16.8 - - + -
240A GLN* 4.0 6.7 - - + -
259A VAL* 3.8 14.6 - - + -
260A LYS 3.9 7.6 - - - -
267A VAL* 4.5 2.7 - - + -
298A PHE* 3.5 26.5 - + - +
299A TYR* 3.2 5.8 + - - -
300A GLN* 2.8 58.1 + - + +
302A VAL* 3.8 13.5 - - + -
309A ALA 3.6 1.8 + - - -
310A ARG* 1.3 70.9 - - - +
312A HIS* 1.3 63.3 + - - +
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU 3.3 10.6 + - - +
238A PHE* 4.1 6.1 - - + -
239A SER* 3.0 43.3 + - - -
240A GLN* 3.0 21.8 + - - +
270A GLU* 5.2 3.1 - - - -
297A ILE* 3.8 31.3 - - + +
298A PHE* 3.3 13.2 - - - +
299A TYR* 4.0 12.8 - + + -
310A ARG* 3.3 33.5 + - - +
311A PHE* 1.3 77.0 - - - +
313A GLY* 1.3 68.7 + - - +
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Residues in contact with GLY 313 (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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240A GLN 3.1 14.6 - - - -
297A ILE* 3.2 11.6 - - - +
298A PHE* 2.8 48.1 + - - -
312A HIS* 1.3 88.0 - - - +
314A ARG* 1.3 57.9 + - - -
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Residues in contact with ARG 314 (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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240A GLN 2.9 5.5 + - - -
241A GLU* 3.0 42.4 + - - +
242A CYS* 2.8 32.4 + - - +
295A SER* 4.1 15.3 - - - -
296A PHE 3.3 10.8 - - - +
297A ILE* 3.5 21.5 - - + +
298A PHE* 3.9 1.7 - - - -
313A GLY* 1.3 75.0 - - - -
315A VAL* 1.3 62.3 + - - +
316A THR* 3.8 17.7 + - - +
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Residues in contact with VAL 315 (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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221A SER* 6.0 0.4 - - - -
242A CYS* 3.3 20.9 - - + +
244A ASN* 3.6 29.8 - - - +
255A VAL* 5.1 0.4 - - + -
258A THR* 5.5 4.9 - - - +
259A VAL* 4.0 18.8 - - + -
295A SER* 3.1 7.4 - - - -
296A PHE* 2.9 75.1 + - + +
298A PHE* 4.1 6.5 - - + -
314A ARG* 1.3 73.0 - - - +
316A THR* 1.3 62.0 + - - +
317A GLN* 5.6 1.3 - - + +
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Residues in contact with THR 316 (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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241A GLU* 4.3 5.7 + - - -
242A CYS 2.9 10.6 + - - -
243A LEU* 3.8 18.1 - - + -
244A ASN* 2.9 28.9 + - - +
293A GLU* 3.5 35.9 - - + +
294A VAL 3.7 3.8 - - - +
295A SER* 4.1 3.3 - - - -
314A ARG* 3.8 23.2 + - - +
315A VAL* 1.3 75.0 - - - +
317A GLN* 1.3 61.0 + - - +
318A PRO* 3.4 4.9 - - + +
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Residues in contact with GLN 317 (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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244A ASN* 3.0 30.1 + - - +
245A LYS 2.8 27.4 + - - +
247A ILE* 3.5 28.9 - - + +
255A VAL* 3.7 27.4 - - + +
285A TRP* 5.5 0.7 - - + -
293A GLU* 3.4 3.9 - - - -
294A VAL* 2.8 47.7 + - + +
295A SER* 5.6 0.7 - - - -
296A PHE* 6.4 0.9 - - + -
315A VAL* 4.2 1.5 - - + -
316A THR* 1.3 71.8 - - - +
318A PRO* 1.3 86.5 + - - +
319A LEU* 3.9 7.3 - - + +
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Residues in contact with PRO 318 (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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243A LEU* 3.8 16.4 - - + -
244A ASN 3.3 24.9 - - - +
246A PRO* 3.3 24.1 - - + +
247A ILE 3.3 1.6 + - - -
292A ASN 4.3 1.3 - - - +
293A GLU* 4.1 21.9 - - + +
316A THR* 3.4 9.0 - - + +
317A GLN* 1.3 107.1 + - - +
319A LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 319 (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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246A PRO* 4.7 3.1 - - - +
247A ILE* 3.2 28.3 - - + +
248A ASN 4.4 0.9 - - - +
249A HIS* 3.9 12.1 - - + +
253A LEU* 3.8 24.2 - - + -
287A LEU* 3.5 34.5 - - + -
291A THR 4.0 0.7 - - - +
292A ASN* 3.2 54.0 + - - +
293A GLU* 3.8 5.8 - - - +
294A VAL 4.8 0.2 - - - +
317A GLN* 3.9 10.3 - - + +
318A PRO* 1.3 86.8 - - - +
320A LYS* 1.3 60.4 + - - +
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.5 35.6 + - + +
247A ILE* 2.9 19.1 + - - +
248A ASN* 3.3 25.5 - - - +
249A HIS* 2.7 29.7 + - - +
292A ASN* 5.2 2.2 - - - +
319A LEU* 1.3 75.6 - - - +
321A GLU* 1.3 63.7 + - - +
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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