Contacts of the strand formed by residues 314 - 321 (chain B) in PDB entry 1QM4
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 ARG 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TYR* 3.0 22.8 + - + +
143B ALA 3.3 9.6 - - - +
144B THR* 4.2 5.6 - - - +
195B ALA* 3.2 26.9 - - + +
196B VAL* 3.2 28.2 - - - +
275B TRP* 3.6 23.6 + - - +
307B VAL* 4.4 0.2 - - - +
312B CYS* 3.5 2.4 - - - -
313B ARG* 1.3 82.1 - - + +
315B VAL* 1.3 63.3 + - - +
335B THR* 3.5 22.0 - - - +
336B TYR* 3.0 58.0 + - + +
338B THR* 3.2 15.3 + - + +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 3.8 0.2 - - - +
142B TYR* 3.3 12.7 - - - -
143B ALA 2.8 29.8 + - - +
303B ALA* 3.7 19.0 - - + +
306B LEU* 4.2 10.8 - - + -
307B VAL* 3.4 18.2 - - + -
312B CYS* 3.2 32.5 - - - -
314B ARG* 1.3 73.2 - - - +
316B LEU* 1.3 66.8 + - - +
317B VAL* 4.6 3.1 - - + +
333B ILE* 3.6 30.1 - - + -
334B PHE 3.4 9.9 - - - +
335B THR* 4.3 2.5 - - - +
336B TYR* 4.4 1.8 - - - -
346B LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 316 (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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140B PHE* 4.1 23.6 - - + -
141B GLY 3.1 24.7 - - - +
142B TYR* 4.1 14.4 - - + -
276B GLY* 4.2 13.2 - - - -
277B ALA* 4.2 14.6 - - + +
315B VAL* 1.3 74.0 - - - +
317B VAL* 1.3 63.0 + - - +
318B GLN* 4.6 0.9 - - - +
334B PHE* 2.8 66.3 + - + +
336B TYR* 3.4 26.5 - - + +
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET 4.1 0.2 - - - +
140B PHE* 3.4 3.3 - - - +
141B GLY 2.6 34.1 + - - +
299B ALA* 3.5 21.5 - - + +
302B VAL* 3.7 19.7 - - + -
303B ALA* 3.4 38.6 - - + -
306B LEU* 5.1 0.2 - - + -
315B VAL* 4.8 6.1 - - + -
316B LEU* 1.3 74.3 - - - +
318B GLN* 1.3 67.7 + - - +
319B VAL* 4.2 3.5 + - + +
331B ILE* 4.4 8.3 - - + -
332B SER 3.4 3.8 - - - +
333B ILE* 3.7 23.8 - - + -
356B LEU* 5.9 0.9 - - + -
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Residues in contact with GLN 318 (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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19A PHE* 4.5 5.1 - - - -
20A MET* 2.7 30.5 + - - +
21A PHE* 4.0 13.5 - - - -
138B LEU* 3.3 25.4 - - + +
139B MET 3.6 2.7 - - - -
140B PHE* 3.5 27.9 - - + -
316B LEU* 4.6 2.6 - - + +
317B VAL* 1.3 73.9 - - - +
319B VAL* 1.3 60.0 + - - +
320B SER* 4.7 1.2 + - - -
330B SER* 3.8 1.4 + - - +
331B ILE* 3.2 3.6 - - - +
332B SER* 2.8 53.7 + - - +
334B PHE* 3.4 24.8 - - + -
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Residues in contact with VAL 319 (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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138B LEU* 3.5 1.9 - - - -
139B MET* 2.7 52.9 + - + +
295B ALA 4.3 4.7 - - - +
298B ALA* 6.1 0.7 - - + -
299B ALA* 3.7 27.4 - - + +
317B VAL* 4.9 3.6 - - + -
318B GLN* 1.3 74.2 - - - +
320B SER* 1.3 59.9 + - - +
321B TYR* 3.4 33.5 - - + +
328B PRO* 3.9 18.2 - - + -
330B SER 4.1 1.6 - - - -
331B ILE* 4.3 9.4 - - + +
356B LEU* 4.7 15.7 - - + -
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Residues in contact with SER 320 (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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20A MET* 3.7 23.0 + - - +
21A PHE* 5.4 0.2 - - - -
22A THR* 4.9 5.4 + - - -
137B GLY 3.6 7.6 - - - -
138B LEU* 3.3 22.7 - - - +
318B GLN* 4.7 1.2 + - - -
319B VAL* 1.3 74.0 - - - +
321B TYR* 1.3 59.2 + - - +
328B PRO* 3.4 8.5 - - - +
329B LEU* 2.7 50.2 + - - -
330B SER 3.0 12.6 + - - -
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Residues in contact with TYR 321 (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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22A THR* 5.7 0.3 + - - -
133B ALA* 3.9 26.7 - - + -
135B ASP 5.0 1.8 - - - +
136B GLN* 3.4 9.0 - - - +
137B GLY* 2.9 34.7 + - - +
139B MET* 4.4 13.0 - - - -
291B VAL* 4.5 7.9 - - + -
295B ALA* 3.5 24.6 - - + +
298B ALA* 5.2 0.5 - - - +
319B VAL* 3.4 29.5 - - + +
320B SER* 1.3 77.0 - - - +
322B ALA* 1.3 60.4 + - - +
325B VAL 5.0 0.9 - - - -
326B ALA 4.1 7.6 - - - -
327B GLU 4.9 0.9 - - - -
328B PRO* 4.0 17.3 - - + -
329B LEU* 4.1 8.6 - - - +
356B LEU* 2.7 35.7 + - - +
358B PRO* 3.8 15.9 - - + -
361B ILE* 3.5 15.1 - - + +
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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