Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 6N8P
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 PRO 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.6 30.1 - - + -
32A PRO* 3.6 10.5 - - + +
34A GLN* 1.3 92.3 - - - +
36A SER* 1.3 59.7 + - - +
49A ILE* 3.9 18.6 - - + -
50A GLY 3.2 10.8 - - - +
51A THR* 4.0 3.4 - - + -
52A ARG* 3.2 17.5 + - - -
333A ILE* 3.2 27.7 - - + +
356A LEU* 4.3 5.6 - - + -
358A GLU* 3.4 20.9 - - + +
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Residues in contact with SER 36 (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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35A PRO* 1.3 77.4 - - - +
37A ALA* 1.3 58.7 + - - +
50A GLY 2.6 11.4 + - - -
51A THR 3.4 16.6 + - - -
52A ARG* 4.0 22.4 - - - +
75A ALA* 4.2 4.0 - - - +
76A VAL 2.4 30.5 + - - +
77A THR* 3.7 10.7 - - - +
333A ILE* 4.0 18.9 - - - +
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Residues in contact with ALA 37 (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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36A SER* 1.3 81.1 - - - +
38A LEU* 1.3 59.8 + - - +
49A ILE* 3.5 1.2 - - - -
50A GLY 3.0 23.6 + - - +
76A VAL* 3.3 17.9 - - + +
77A THR 3.6 19.1 - - - +
78A GLN* 3.9 1.8 - - - +
79A ILE* 3.8 24.5 - - + -
333A ILE 4.3 5.1 + - - -
356A LEU* 3.3 16.0 - - - +
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Residues in contact with LEU 38 (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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37A ALA* 1.3 76.0 - - - +
39A GLY* 1.3 67.3 + - - +
47A LEU* 3.6 28.9 - - + -
48A ALA 3.4 10.3 - - - +
49A ILE* 4.6 0.7 - - + -
79A ILE* 3.8 16.8 + - - +
333A ILE 4.3 2.0 + - - -
334A GLY* 3.6 19.3 - - - +
335A PHE* 3.6 37.5 - - - +
336A THR* 4.2 11.4 - - + +
354A VAL* 4.3 6.7 - - + +
356A LEU* 3.8 29.6 - - + +
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Residues in contact with GLY 39 (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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38A LEU* 1.3 77.1 - - - +
40A TYR* 1.3 62.7 + - - +
47A LEU* 3.6 6.2 - - - +
48A ALA 2.7 39.8 + - - +
79A ILE* 3.8 27.0 - - - +
81A LEU* 3.8 3.8 - - - -
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Residues in contact with TYR 40 (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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38A LEU* 5.7 0.4 - - + -
39A GLY* 1.3 76.9 - - - +
41A SER* 1.3 70.4 + - - +
42A PRO* 3.3 40.2 + - + +
45A ARG* 3.2 36.9 - - + +
46A ILE 3.3 21.3 - - - -
47A LEU* 4.2 15.9 - - + -
81A LEU* 3.4 15.7 + - - +
336A THR* 4.5 21.1 - - + +
337A VAL 5.5 1.1 - - - -
338A LEU* 3.4 47.3 - - + +
339A THR 5.9 0.2 - - - -
351A TYR* 4.7 1.9 + - - -
422A ILE* 4.7 7.2 - - + -
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Residues in contact with SER 41 (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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40A TYR* 1.3 74.2 - - - +
42A PRO* 1.3 59.0 - - - +
43A SER* 3.2 20.1 + - - -
44A LEU* 3.3 24.4 + - - +
45A ARG* 2.7 35.4 + - - -
46A ILE* 3.1 11.2 + - - -
81A LEU* 3.6 31.4 - - - +
82A LEU 4.4 6.9 + - - -
83A PRO* 5.8 0.2 - - - +
85A GLN 4.7 0.7 + - - -
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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