Contacts of the strand formed by residues 327 - 332 (chain 1) in PDB entry 6Q8O
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 327 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991 GLY* 3.1 29.5 - - - +
2531 GLN* 3.2 10.1 - - - +
2911 ILE 3.3 5.9 - - - +
2921 PRO 2.9 10.2 - - - +
2931 GLY 2.6 22.1 + - - +
2941 GLY* 3.7 7.6 - - - -
3251 THR* 3.1 4.8 - - - -
3261 GLY* 1.3 69.0 - - - +
3281 VAL* 1.3 61.4 + - - -
3291 ILE* 3.8 4.3 + - - +
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Residues in contact with VAL 328 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991 GLY 5.2 0.5 - - - +
2531 GLN 2.9 9.3 + - - +
2541 ILE* 3.3 13.3 - - + -
2551 SER* 2.9 30.6 + - - -
2721 PHE* 5.7 3.1 - - + -
2751 LEU* 4.9 8.5 - - + -
2761 ILE* 6.0 2.9 - - + -
2901 ILE* 4.3 11.7 - - + -
2911 ILE 3.0 14.4 - - - +
2921 PRO* 3.3 19.1 - - + +
3111 MET* 3.9 23.8 - - + -
3261 GLY 3.8 9.6 - - - +
3271 GLY* 1.3 73.0 - - - -
3291 ILE* 1.3 63.2 + - - +
3301 LEU* 3.7 22.9 - - + -
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Residues in contact with ILE 329 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981 PRO* 4.3 10.5 - - + +
991 GLY* 3.8 27.4 - - - +
2551 SER* 3.2 20.6 - - - +
2561 GLY* 5.3 0.4 - - - +
2901 ILE* 3.6 1.6 - - - -
2911 ILE* 2.9 42.5 + - + +
2941 GLY 5.8 4.7 - - - +
2951 SER* 6.0 2.2 - - - -
3271 GLY 4.4 3.4 - - - +
3281 VAL* 1.3 75.2 - - - +
3301 LEU* 1.3 73.4 + - - +
3311 ILE* 3.8 2.3 + - + +
862 LEU* 3.7 34.3 - - + -
872 SER* 3.3 29.4 - - - +
902 LEU* 4.7 4.0 - - + -
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Residues in contact with LEU 330 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2541 ILE* 3.6 26.5 - - + -
2551 SER 3.0 16.8 + - - +
2561 GLY* 4.4 5.9 - - - -
2571 PRO* 4.1 9.2 - - + +
2581 VAL* 4.5 17.5 - - + +
2761 ILE* 4.5 19.3 - - + -
2831 PRO* 5.6 1.8 - - + -
2871 ILE* 3.6 28.5 - - + -
2891 ALA 3.8 3.6 - - - +
2901 ILE* 3.6 23.3 - - + -
3281 VAL* 3.7 20.4 - - + -
3291 ILE* 1.3 72.8 - - - +
3311 ILE* 1.3 61.9 + - - +
3321 PRO* 3.8 2.6 - - - +
902 LEU* 3.0 20.3 - - - +
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Residues in contact with ILE 331 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871 ILE* 3.4 3.0 - - - -
2881 GLN* 2.6 56.5 + - + +
2891 ALA* 2.9 22.8 + - + +
2911 ILE* 3.7 27.6 - - + -
3291 ILE* 4.2 12.1 - - + +
3301 LEU* 1.3 76.1 - - - +
3321 PRO* 1.3 58.3 - - + -
3351 VAL* 4.3 4.9 - - + +
3371 MET* 3.9 18.6 - - + -
3401 ALA* 3.6 34.1 - - + -
3411 MET* 5.2 0.7 - - - -
862 LEU* 4.7 3.6 - - + -
902 LEU* 3.8 11.4 - - + -
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Residues in contact with PRO 332 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2571 PRO* 5.0 15.3 - - + -
2851 GLU* 5.3 7.9 - - + -
2861 PRO 3.1 21.1 - - - +
2871 ILE* 3.6 7.6 - - + -
2881 GLN* 2.6 31.4 + - - +
3301 LEU 3.8 2.2 - - - +
3311 ILE* 1.3 88.0 - - + +
3331 GLU* 1.3 56.4 + - - +
3341 ARG* 3.3 16.1 + - + +
3351 VAL* 2.9 19.6 - - + +
4361 LEU* 5.7 4.9 - - + -
902 LEU* 3.6 22.7 - - + +
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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