Contacts of the strand formed by residues 322 - 335 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ARG* 3.3 33.0 + - - +
100B PRO* 3.9 12.8 - - - +
307C GLY 3.4 10.8 - - - -
308C THR* 4.6 1.1 - - - -
320C GLY* 3.7 2.2 - - - -
321C SER* 1.3 81.6 + - - +
323C SER* 1.3 59.7 + - - -
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Residues in contact with SER 323 (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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98B ARG* 3.3 25.4 + - - +
100B PRO* 4.3 3.8 - - - -
118C THR* 4.7 4.7 + - - -
305C ASN* 5.2 1.6 + - - -
306C ALA* 3.4 1.9 - - - +
307C GLY* 2.8 47.6 + - - -
309C MET* 3.4 41.9 - - - +
322C GLY* 1.3 74.3 - - - -
324C TRP* 1.3 60.4 + - - +
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Residues in contact with TRP 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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96B ARG* 3.6 38.6 + - - +
97B GLN* 3.3 8.5 - - - +
98B ARG* 3.1 76.9 + - + +
111B ILE* 3.5 35.7 - - + -
305C ASN* 3.3 14.1 - - - +
306C ALA* 4.5 8.1 - - + -
323C SER* 1.3 74.5 - - - +
325C LEU* 1.3 74.8 + - - +
326C PHE* 4.7 4.6 - - + +
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Residues in contact with LEU 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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95B THR* 4.0 12.3 - - + -
96B ARG 3.4 4.0 - - - +
97B GLN* 3.9 23.8 - - + +
303C THR* 4.2 23.1 - - + +
304C ALA* 3.3 7.6 - - - +
305C ASN* 2.9 54.2 + - - +
324C TRP* 1.3 78.5 - - - +
326C PHE* 1.3 66.4 + - - +
327C GLN* 3.8 34.8 - - + +
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Residues in contact with PHE 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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95B THR* 3.4 3.8 - - - -
96B ARG* 2.8 56.0 + - + +
302C LEU* 3.6 31.0 - - + -
303C THR 3.9 1.1 - - - -
304C ALA* 4.5 8.7 - - + -
324C TRP* 4.9 5.6 - - + +
325C LEU* 1.3 75.5 - - - +
327C GLN* 1.3 60.0 + - - +
328C PRO* 3.5 31.1 - - + +
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Residues in contact with GLN 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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94B GLY 3.3 14.4 - - - +
95B THR* 3.5 27.4 + - + +
301C SER* 4.7 0.3 + - - -
302C LEU* 3.7 2.5 - - - +
303C THR* 2.7 57.0 + - - +
325C LEU* 3.8 20.6 - - + +
326C PHE* 1.3 74.4 - - - +
328C PRO* 1.4 64.0 - - - +
329C SER* 4.0 8.0 + - - +
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Residues in contact with PRO 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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93B SER 3.8 1.4 - - - -
94B GLY* 3.1 40.1 + - - +
115B TYR* 5.9 3.4 - - + -
300C ILE* 6.2 2.2 - - + -
301C SER 3.4 10.3 - - - +
302C LEU* 3.9 13.0 - - + -
326C PHE* 3.5 32.3 - - + +
327C GLN* 1.4 86.0 - - - +
329C SER* 1.3 66.1 + - - +
330C ILE* 6.4 0.9 - - + -
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Residues in contact with SER 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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92B GLY 3.3 10.1 - - - -
93B SER* 4.4 8.2 + - - -
94B GLY 5.2 0.2 + - - -
299C SER 4.4 1.1 - - - -
300C ILE* 3.4 1.2 - - - +
301C SER* 2.8 47.7 + - - +
327C GLN* 4.1 9.2 + - - +
328C PRO* 1.3 79.3 + - - +
330C ILE* 1.3 69.8 + - - +
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Residues in contact with ILE 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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90B VAL 3.6 1.0 - - - +
91B ASP* 3.4 4.2 - - - +
92B GLY* 2.7 45.0 + - - +
298C PRO* 3.8 26.5 - - + -
299C SER 3.5 4.3 - - - +
300C ILE* 3.9 28.0 - - + -
328C PRO* 6.4 0.7 - - + -
329C SER* 1.3 80.2 - - - +
331C ASN* 1.3 65.8 + - - +
332C LEU* 5.0 1.8 - - + +
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Residues in contact with ASN 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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89B GLY* 4.6 4.9 - - - -
90B VAL 3.3 12.7 + - - +
91B ASP* 2.7 35.2 + - - +
298C PRO* 3.3 2.2 - - - +
299C SER* 2.8 44.5 + - - +
330C ILE* 1.3 75.5 - - - +
332C LEU* 1.3 61.6 + - - +
333C PRO* 3.8 16.8 - - - +
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Residues in contact with LEU 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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89B GLY* 3.3 1.2 - - - -
90B VAL* 2.7 49.5 + - + +
296C PHE 3.5 20.2 - - - +
298C PRO* 3.9 26.9 - - + -
330C ILE* 4.3 1.9 - - + +
331C ASN* 1.3 75.3 - - - +
333C PRO* 1.3 88.7 - - + +
334C ILE* 3.5 17.3 + - + +
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Residues in contact with PRO 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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87B ARG* 4.6 13.2 - - + +
88B ILE 4.3 0.7 - - - +
89B GLY* 4.2 5.4 - - - -
295C ALA 3.5 21.5 - - - +
296C PHE 4.0 8.7 - - - +
297C PHE 4.1 5.2 - - - +
299C SER* 6.3 0.2 - - - -
331C ASN* 3.8 17.0 - - - +
332C LEU* 1.3 105.9 - - + +
334C ILE* 1.3 62.2 - - - +
336C THR* 4.6 10.1 - - + -
340C LEU* 3.8 22.9 - - + -
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Residues in contact with ILE 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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88B ILE* 2.9 20.5 + - + +
89B GLY* 3.9 4.7 - - - -
90B VAL* 3.6 31.2 - - + -
119B LEU* 4.0 11.9 - - + -
332C LEU* 3.5 18.6 + - + +
333C PRO* 1.3 82.8 - - - +
335C PHE* 1.3 64.1 + - + +
336C THR* 4.1 1.5 + - - -
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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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85B PHE* 4.6 10.3 - + + -
86B PRO* 3.5 23.6 - - + -
87B ARG* 3.4 5.0 - - - +
88B ILE* 2.6 63.8 + - + +
334C ILE* 1.3 77.6 - - + +
336C THR* 1.3 73.6 + - - +
337C ALA* 4.0 26.7 - - + -
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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