Contacts of the strand formed by residues 322 - 335 (chain A) in PDB entry 3D5K
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 GLY 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A GLY 3.4 10.5 - - - -
308A THR* 4.5 3.5 - - - +
318A ASP 4.9 0.4 + - - -
320A GLY* 3.4 5.7 - - - +
321A SER* 1.3 82.8 + - - +
323A SER* 1.3 59.8 + - - -
98C ARG* 4.5 10.9 - - - +
99C LEU 4.8 0.9 - - - -
100C PRO* 3.8 13.0 - - - +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 5.2 2.8 + - - -
305A ASN* 5.3 2.0 + - - -
306A ALA* 3.4 2.8 - - - +
307A GLY 3.0 36.8 + - - +
308A THR 3.8 1.6 - - - -
309A MET* 3.2 44.5 + - - +
322A GLY* 1.3 75.3 - - - -
324A TRP* 1.3 68.7 + - - +
98C ARG* 3.4 18.8 - - - -
100C PRO* 4.4 3.4 - - - -
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Residues in contact with TRP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASN* 3.3 17.7 - - - +
306A ALA* 4.2 7.6 - - + +
323A SER* 1.3 79.0 - - - +
325A LEU* 1.3 65.3 - - - +
326A PHE* 4.8 2.7 - - + -
96C ARG* 3.9 23.1 + - - +
97C GLN* 3.3 18.5 - - - +
98C ARG* 3.4 60.3 + - + +
111C ILE* 4.0 20.1 - - + +
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Residues in contact with LEU 325 (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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303A THR* 4.2 18.8 - - + +
304A ALA* 3.1 6.1 - - - +
305A ASN* 3.0 55.4 + - - +
324A TRP* 1.3 77.3 - - - +
326A PHE* 1.3 68.6 + - - +
327A GLN* 4.4 21.8 - - + +
95C THR* 4.1 22.0 - - + -
96C ARG 3.9 4.3 - - - +
97C GLN* 3.9 26.5 - - + +
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Residues in contact with PHE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.7 27.1 - - + -
303A THR 3.6 1.3 - - - -
304A ALA* 3.9 17.9 - - + -
324A TRP* 5.5 3.1 - - + -
325A LEU* 1.3 75.3 - - - +
327A GLN* 1.3 61.4 + - - +
328A PRO* 3.6 28.5 - - + +
95C THR* 3.6 2.6 - - - -
96C ARG* 3.1 41.9 + - + +
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Residues in contact with GLN 327 (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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301A SER 3.8 1.4 - - - +
302A LEU* 3.8 2.8 - - - +
303A THR* 2.7 52.7 + - - +
325A LEU* 4.4 18.2 - - + +
326A PHE* 1.3 75.7 - - - +
328A PRO* 1.3 67.1 - - - +
329A SER* 4.1 7.6 + - - +
93C SER* 5.5 2.9 - - - +
94C GLY 3.2 12.1 - - - +
95C THR* 3.6 26.1 + - + +
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Residues in contact with PRO 328 (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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300A ILE* 6.0 2.9 - - + -
301A SER 3.6 5.4 - - - +
302A LEU* 3.9 16.1 - - + -
326A PHE* 3.6 26.9 - - + +
327A GLN* 1.3 88.8 - - - +
329A SER* 1.3 62.9 + - - +
330A ILE* 5.4 6.5 - - + -
93C SER* 3.8 0.5 + - - -
94C GLY* 3.0 48.1 + - - +
115C TYR* 6.3 1.3 - - + -
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Residues in contact with SER 329 (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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299A SER 4.5 0.4 - - - -
300A ILE* 3.4 7.8 - - - +
301A SER* 2.8 44.2 + - - -
327A GLN* 4.1 9.0 + - - +
328A PRO* 1.3 77.1 + - - +
330A ILE* 1.3 73.6 + - - +
92C GLY 3.3 9.8 + - - -
93C SER* 4.8 5.5 + - - -
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Residues in contact with ILE 330 (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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298A PRO* 4.1 25.1 - - + -
299A SER 3.5 6.3 - - - +
300A ILE* 4.1 20.2 - - + -
328A PRO* 5.4 4.7 - - + -
329A SER* 1.3 85.0 - - - +
331A ASN* 1.3 64.5 + - - +
332A LEU* 5.1 2.7 - - + +
90C VAL 3.7 1.1 - - - +
91C ASP* 3.5 4.0 - - - +
92C GLY* 2.8 51.0 + - - +
93C SER 6.4 0.2 - - - -
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Residues in contact with ASN 331 (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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298A PRO* 3.3 4.1 - - - +
299A SER* 2.7 51.1 + - - +
330A ILE* 1.3 75.7 - - - +
332A LEU* 1.3 63.1 + - - +
333A PRO* 3.9 21.1 - - - +
89C GLY* 5.1 4.1 - - - -
90C VAL 3.4 5.1 + - - +
91C ASP* 2.6 30.0 + - - +
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Residues in contact with LEU 332 (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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296A PHE 3.4 25.8 - - - +
298A PRO* 3.9 30.3 - - + -
330A ILE* 4.3 2.4 - - + +
331A ASN* 1.3 76.8 - - - +
333A PRO* 1.3 72.4 - - + +
334A ILE* 3.7 18.5 - - + +
89C GLY* 3.2 0.7 - - - -
90C VAL* 2.8 47.9 + - + +
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Residues in contact with PRO 333 (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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295A ALA 3.6 22.9 - - - +
296A PHE* 4.3 7.0 - - - +
297A PHE 4.4 4.7 - - - +
299A SER* 6.2 0.9 - - - -
331A ASN* 3.9 16.4 - - - +
332A LEU* 1.3 98.9 - - + +
334A ILE* 1.3 65.2 + - - +
336A THR* 4.9 10.1 - - + -
340A LEU* 3.9 20.9 - - + -
87C ARG* 5.7 9.0 - - + +
88C ILE 4.1 5.4 - - - +
89C GLY* 4.2 2.9 - - - -
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Residues in contact with ILE 334 (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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332A LEU* 3.7 28.0 - - + +
333A PRO* 1.3 84.6 - - - +
335A PHE* 1.3 65.6 + - + +
336A THR* 3.9 3.2 + - - -
88C ILE* 2.9 12.5 + - + +
89C GLY* 3.8 6.3 - - - -
90C VAL* 3.8 25.8 - - + -
119C LEU* 4.4 9.2 - - + -
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Residues in contact with PHE 335 (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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333A PRO* 5.7 0.2 - - - +
334A ILE* 1.3 78.3 - - + +
336A THR* 1.3 76.0 + - - +
337A ALA* 4.2 21.1 - - + -
85C PHE* 4.1 22.9 - + + -
86C PRO* 3.2 32.1 - - + -
87C ARG* 3.7 1.7 - - - +
88C ILE* 2.8 60.6 + - + +
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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