Contacts of the strand formed by residues 423 - 431 (chain D) in PDB entry 1QQW
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 ILE 423 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428C GLU* 4.2 3.6 - - - -
429C VAL* 2.9 28.2 + - + +
221D LYS* 4.1 18.4 - - + +
231D TYR* 4.1 21.3 - - + +
286D PHE* 4.2 11.7 - - + -
347D PRO* 5.9 1.6 - - + -
421D HIS* 3.4 31.2 + - + +
422D SER* 1.3 72.4 + - - +
424D GLN* 1.3 70.9 + - - +
425D TYR* 3.3 41.8 - - + +
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Residues in contact with GLN 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C SER* 4.2 7.2 + - - -
427C GLY* 3.5 26.9 - - - +
428C GLU* 3.6 24.1 - - + +
423D ILE* 1.3 83.0 - - - +
425D TYR* 1.3 80.9 + - - +
426D SER* 4.5 3.1 - - - -
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Residues in contact with TYR 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.3 17.3 - - + -
47A ARG 3.5 17.9 - - - -
48A GLY* 3.5 16.2 - - - -
49A PRO* 3.3 27.3 - - + +
44B VAL* 4.8 2.2 - - + -
53B GLN* 4.8 3.9 + - - -
426C SER* 3.6 0.6 - - - -
427C GLY 3.1 26.7 + - - +
429C VAL* 3.3 32.1 - - + -
347D PRO* 3.2 25.8 - - + +
423D ILE* 3.3 40.1 - - + +
424D GLN* 1.3 84.7 - - - +
426D SER* 1.3 66.9 + - - +
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Residues in contact with SER 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.5 7.2 + - - +
45A GLY* 4.2 9.0 - - - -
46A PRO* 5.2 2.6 - - - +
424C GLN* 3.7 9.9 + - - -
425C TYR 3.6 8.3 - - - -
426C SER* 3.5 20.3 + - - -
424D GLN* 4.5 3.1 - - - -
425D TYR* 1.3 80.9 - - - +
427D GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.2 4.7 - - - +
45A GLY* 4.3 8.1 - - - -
46A PRO* 5.7 0.7 - - - -
424C GLN* 3.1 21.4 - - - +
425C TYR* 3.1 29.1 + - - +
426D SER* 1.3 78.4 + - - +
428D GLU* 1.3 65.5 + - - -
429D VAL* 4.6 0.2 - - - +
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Residues in contact with GLU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 2.7 27.4 + - - +
422C SER* 3.7 22.1 - - - +
423C ILE 3.5 9.2 - - - +
424C GLN* 4.0 17.0 - - + +
427D GLY* 1.3 73.3 - - - -
429D VAL* 1.3 59.2 + - - +
430D ARG* 2.9 43.5 + - + -
432D PHE* 3.3 12.9 - - + -
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Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.4 14.9 - - + +
43A THR 3.4 4.7 - - - +
44A VAL* 4.2 15.7 - - + -
51A LEU* 3.3 40.2 - - + -
53A GLN* 4.1 6.7 - - - +
44B VAL* 6.0 0.4 - - + -
49B PRO* 5.1 3.6 - - + -
421C HIS 4.6 2.8 - - - +
422C SER* 2.7 21.0 + - - -
423C ILE 3.1 9.2 + - - +
425C TYR* 3.3 40.4 - - + -
427D GLY 4.6 0.2 - - - +
428D GLU* 1.3 74.5 - - - +
430D ARG* 1.3 55.9 + - - +
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Residues in contact with ARG 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.6 9.8 - - - -
43A THR 3.3 22.4 + - - -
419C LEU* 6.2 3.8 - - + -
420C GLU* 6.0 0.9 - - - -
422C SER* 2.9 22.4 + - - +
428D GLU* 2.9 37.7 + - + -
429D VAL* 1.3 70.5 - - - +
431D ARG* 1.3 68.2 + - - +
432D PHE* 3.2 50.9 + - + +
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Residues in contact with ARG 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 5.8 0.4 - - - -
37A ASP* 3.4 52.6 + - + +
40A ASN* 3.0 36.0 + - + +
41A VAL* 3.4 6.7 - - - +
42A ILE* 3.7 17.1 - - + +
54A ASP* 3.0 43.4 + - - +
56A VAL* 3.7 20.1 - - - +
419C LEU* 4.7 10.5 - - + +
420C GLU* 3.0 42.0 + - - +
159D ILE* 4.5 4.4 - - - +
430D ARG* 1.3 80.0 - - - +
432D PHE* 1.3 62.6 + - - +
433D ASN* 3.3 4.2 + - - +
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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