Contacts of the strand formed by residues 314 - 321 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 6.1 0.2 - - - -
142A TYR* 3.0 24.1 + - + +
143A ALA 3.4 7.9 - - - +
144A THR* 4.1 5.4 - - - +
195A ALA* 3.2 29.5 - - + +
196A VAL* 3.3 26.3 - - - +
275A TRP* 3.6 23.6 + - - +
312A CYS* 3.5 2.0 - - - -
313A ARG* 1.3 83.1 - - + +
315A VAL* 1.3 63.5 + - - +
335A THR* 3.4 22.7 - - - +
336A TYR* 2.9 61.3 + - + +
338A THR* 3.2 10.2 + - + +
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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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142A TYR* 3.2 14.2 - - - -
143A ALA 2.9 29.4 + - - +
303A ALA* 3.8 19.7 - - + +
306A LEU* 4.1 13.0 - - + -
307A VAL* 3.4 16.2 - - + -
312A CYS* 3.3 29.6 - - - -
314A ARG* 1.3 74.9 - - - +
316A LEU* 1.3 66.8 + - - +
317A VAL* 3.9 3.6 - - + +
333A ILE* 3.7 31.0 - - + -
334A PHE 3.5 9.2 - - - +
335A THR* 4.3 2.9 - - - +
336A TYR* 4.4 1.3 - - - -
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Residues in contact with LEU 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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140A PHE* 4.1 25.6 - - + -
141A GLY 3.1 23.8 - - - +
142A TYR* 4.1 11.7 - - + -
276A GLY* 4.2 17.9 - - - -
277A ALA* 4.2 10.3 - - + +
315A VAL* 1.3 72.9 - - - +
317A VAL* 1.3 62.6 + - - +
318A GLN* 4.6 1.3 - - - +
334A PHE* 2.9 61.2 + - + +
336A TYR* 3.4 26.0 - - + +
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Residues in contact with VAL 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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139A MET 4.1 0.2 - - - +
140A PHE* 3.3 3.5 - - - +
141A GLY 2.6 34.3 + - - +
299A ALA* 3.5 21.3 - - + +
302A VAL* 3.7 21.3 - - + -
303A ALA* 3.4 37.7 - - + -
306A LEU* 5.1 0.4 - - + -
315A VAL* 4.8 5.6 - - + -
316A LEU* 1.3 72.7 - - - +
318A GLN* 1.3 64.5 + - - +
319A VAL* 4.2 3.5 + - + +
331A ILE* 4.3 10.5 - - + -
332A SER 3.4 4.0 - - - +
333A ILE* 3.7 23.6 - - + +
356A LEU* 5.9 0.9 - - + -
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Residues in contact with GLN 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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138A LEU* 3.3 25.8 - - + +
139A MET 3.6 3.4 - - - -
140A PHE* 3.6 26.4 - - + -
316A LEU* 4.6 2.2 - - + +
317A VAL* 1.3 75.3 - - - +
319A VAL* 1.3 59.2 + - - +
320A SER* 4.8 1.6 + - - +
330A SER* 3.8 2.0 + - - +
331A ILE* 3.2 3.2 - - - +
332A SER* 2.7 50.8 + - - +
334A PHE* 3.4 25.6 - - + -
19B PHE* 4.2 7.9 - - - -
20B MET 2.6 33.1 + - - +
21B PHE* 3.9 12.7 - - - -
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Residues in contact with VAL 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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138A LEU* 3.5 1.8 - - - -
139A MET* 2.7 51.5 + - + +
295A ALA 4.3 4.7 - - - +
298A ALA* 6.1 0.7 - - + -
299A ALA* 3.7 28.3 - - + +
317A VAL* 4.9 4.7 - - + -
318A GLN* 1.3 72.9 - - - +
320A SER* 1.3 61.0 + - - +
321A TYR* 3.4 33.5 - - + +
328A PRO* 4.0 17.5 - - + -
330A SER 4.0 1.6 - - - -
331A ILE* 4.3 10.3 - - + +
356A LEU* 4.7 14.8 - - + -
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Residues in contact with SER 320 (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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137A GLY 3.5 8.0 + - - -
138A LEU* 3.4 21.8 - - - +
318A GLN* 4.8 1.2 + - - -
319A VAL* 1.3 72.8 - - - +
321A TYR* 1.3 59.3 + - - +
328A PRO* 3.4 7.4 - - - +
329A LEU* 2.6 50.8 + - - -
330A SER 3.0 12.6 + - - -
20B MET* 3.4 25.2 + - - +
22B THR* 4.8 4.8 + - - -
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Residues in contact with TYR 321 (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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133A ALA* 3.9 28.0 - - + -
135A ASP 5.0 2.0 - - - +
136A GLN* 3.4 9.7 - - - +
137A GLY* 2.9 34.2 + - - +
139A MET* 4.4 12.1 - - - -
291A VAL* 4.6 6.1 - - + -
295A ALA* 3.5 23.3 - - + +
298A ALA* 5.2 0.5 - - - +
319A VAL* 3.4 30.0 - - + +
320A SER* 1.3 77.5 - - - +
322A ALA* 1.3 61.0 + - - +
325A VAL 4.9 0.4 - - - -
326A ALA 4.1 7.9 - - - -
327A GLU 4.9 0.9 - - - -
328A PRO* 4.0 16.4 - - + -
329A LEU* 4.0 8.0 - - - +
356A LEU* 2.6 34.9 + - - +
358A PRO* 3.8 17.9 - - + -
361A ILE* 3.4 15.5 - - + +
22B THR* 5.4 0.5 + - - -
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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