Contacts of the strand formed by residues 322 - 335 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ARG* 4.1 25.1 + - - +
100A PRO* 4.1 13.0 - - - +
307B GLY 3.4 9.4 - - - -
308B THR* 4.8 2.2 - - - +
318B ASP 4.9 0.2 + - - -
320B GLY* 3.3 6.1 - - - +
321B SER* 1.3 80.2 + - - +
323B SER* 1.3 60.1 + - - -
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 3.4 22.2 - - - +
100A PRO* 4.3 2.5 - - - -
118B THR* 5.9 1.4 - - - -
305B ASN* 5.4 1.0 + - - -
306B ALA* 3.4 2.9 - - - +
307B GLY 2.8 35.0 + - - +
308B THR 3.6 13.3 + - - -
309B MET* 3.5 40.3 - - - +
322B GLY* 1.3 74.1 - - - -
324B TRP* 1.3 62.8 + - - +
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Residues in contact with TRP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 3.7 31.5 + - - +
97A GLN* 3.2 23.3 - - - +
98A ARG* 3.4 44.4 + - + +
111A ILE* 3.7 35.2 - - + -
305B ASN* 3.4 17.9 - - - +
306B ALA* 4.1 7.9 - - + +
309B MET* 5.5 1.6 - - - +
323B SER* 1.3 77.3 - - - +
325B LEU* 1.3 69.2 + - - +
326B PHE* 4.4 4.7 - - + +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 4.3 10.3 - - + -
96A ARG 3.6 4.9 - - - +
97A GLN* 3.8 29.2 - - + +
303B THR* 4.2 20.2 - - + +
304B ALA* 3.3 7.1 - - - +
305B ASN* 3.0 57.4 + - - +
324B TRP* 1.3 77.5 - - - +
326B PHE* 1.3 66.6 + - - +
327B GLN* 3.7 35.0 - - + +
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 3.5 3.3 - - - -
96A ARG* 2.9 52.8 + - + +
302B LEU* 3.7 33.7 - - + -
303B THR 3.8 1.3 - - - -
304B ALA* 4.4 9.4 - - + -
324B TRP* 5.0 5.6 - - + +
325B LEU* 1.3 75.0 - - - +
327B GLN* 1.3 59.4 + - - +
328B PRO* 3.5 30.4 - - + +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 3.4 14.1 - - - +
95A THR* 3.7 26.8 + - + +
301B SER* 4.9 0.3 + - - -
302B LEU* 4.0 1.9 - - - +
303B THR* 2.9 49.7 + - - +
325B LEU* 3.7 23.8 - - + +
326B PHE* 1.3 73.6 - - - +
328B PRO* 1.4 67.0 - - - +
329B SER* 3.9 7.7 + - - +
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Residues in contact with PRO 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 3.7 1.2 - - - -
94A GLY* 3.1 42.1 + - - +
300B ILE* 6.1 2.7 - - + -
301B SER 3.3 10.8 - - - +
302B LEU* 3.9 12.1 - - + -
326B PHE* 3.5 32.8 - - + +
327B GLN* 1.4 87.2 - - - +
329B SER* 1.3 67.1 + - - +
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 5.5 5.8 - - - -
92A GLY 3.5 7.9 - - - -
93A SER* 4.8 6.8 - - - -
299B SER 3.6 0.4 - - - +
300B ILE* 3.4 6.2 - - - +
301B SER* 2.8 55.0 + - - +
327B GLN* 3.9 8.7 + - - +
328B PRO* 1.3 77.6 + - - +
330B ILE* 1.3 63.2 - - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL 3.6 1.1 - - - +
91A ASP* 3.5 4.7 - - - +
92A GLY* 2.8 58.9 + - - +
298B PRO* 3.7 28.7 - - + -
299B SER 3.2 9.0 - - - +
300B ILE* 4.2 18.6 - - + -
329B SER* 1.3 75.8 - - - +
331B ASN* 1.3 65.4 + - - +
332B LEU* 5.0 1.6 - - + +
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 6.2 0.7 - - - -
89A GLY* 4.6 10.7 - - - -
90A VAL 3.3 12.4 + - - -
91A ASP* 3.1 27.1 + - - +
298B PRO* 3.4 2.4 - - - +
299B SER* 2.8 45.1 + - - +
330B ILE* 1.3 73.1 - - - +
332B LEU* 1.3 60.6 + - - +
333B PRO* 3.7 21.0 - - - +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 2.8 49.6 + - + +
296B PHE 3.7 19.5 - - - +
297B PHE* 4.4 0.2 - - - -
298B PRO* 3.7 37.7 - - + -
330B ILE* 4.3 2.6 - - + +
331B ASN* 1.3 75.0 - - - +
333B PRO* 1.3 69.3 - - - +
334B ILE* 3.5 17.2 + - + +
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Residues in contact with PRO 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 5.2 10.8 - - + +
88A ILE 4.3 1.3 - - - +
89A GLY* 4.1 6.3 - - - -
295B ALA 3.7 24.0 - - - +
296B PHE 4.3 6.3 - - - +
297B PHE 4.3 6.5 - - - +
299B SER* 6.2 0.2 - - - -
331B ASN* 3.7 18.6 - - - +
332B LEU* 1.3 95.9 - - + +
334B ILE* 1.3 66.4 + - - +
336B THR* 4.9 9.4 - - + -
340B LEU* 3.8 23.3 - - + -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 2.9 17.9 + - + +
89A GLY* 3.9 7.0 - - - -
90A VAL* 3.8 24.9 - - + -
119A LEU* 4.2 10.8 - - + -
332B LEU* 3.7 24.5 - - + +
333B PRO* 1.3 83.3 - - - +
335B PHE* 1.3 63.1 + - + +
336B THR* 4.2 2.1 + - - -
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.4 13.5 - + + -
86A PRO* 3.4 22.2 - - + -
87A ARG* 3.5 4.2 - - - -
88A ILE* 2.7 60.1 + - + +
334B ILE* 1.3 76.7 - - + +
336B THR* 1.3 63.3 + - - +
337B ALA* 3.6 35.4 - - + -
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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