Contacts of the strand formed by residues 40 - 52 (chain A) in PDB entry 5JTP
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 VAL 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.6 8.0 + - + +
39A GLU* 1.3 68.5 - - - +
41A LYS* 1.3 59.4 - - - +
42A LEU* 6.3 0.4 - - + -
64A VAL* 4.7 4.3 - - + -
65A THR 3.4 7.9 - - - +
66A ALA* 4.4 11.7 - - + -
74A PHE* 5.1 1.6 - - + -
126A LEU* 3.6 40.8 - - + -
128A LEU* 5.4 2.5 - - + -
465E LYS* 4.0 1.0 - - - +
466E ALA* 2.7 56.7 + - + +
467E ALA* 5.3 1.3 - - - +
468E LEU 5.2 4.9 - - - +
470E LEU* 3.6 31.0 - - + -
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Residues in contact with LYS 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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39A GLU* 3.0 27.3 + - + +
40A VAL* 1.3 74.5 - - - +
42A LEU* 1.3 69.1 + - - +
43A ASP* 2.8 40.1 + - - +
64A VAL* 3.9 1.1 - - - +
65A THR* 2.9 53.4 + - + +
67A SER* 5.8 3.1 - - - -
463E THR* 5.6 4.7 - - + -
464E MET 4.4 4.5 - - - +
465E LYS* 4.8 15.5 - - + +
466E ALA 4.8 0.4 - - - +
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Residues in contact with LEU 42 (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 VAL* 4.0 2.0 + - + +
41A LYS* 1.3 77.9 - - - +
43A ASP* 1.3 65.1 + - - +
44A LEU* 3.9 21.1 - - + -
62A VAL* 3.5 28.5 - - + -
63A THR 3.5 15.7 - - - +
64A VAL* 3.7 14.4 - - + +
107A PHE* 4.8 7.4 - - + -
128A LEU* 4.2 24.2 - - + -
131A VAL* 5.0 3.8 - - + -
463E THR* 3.1 32.3 - - - +
464E MET* 3.0 43.1 + - + +
466E ALA* 5.3 2.5 - - + +
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Residues in contact with ASP 43 (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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41A LYS* 2.8 35.1 + - - +
42A LEU* 1.3 77.0 - - - +
44A LEU* 1.3 63.0 + - - +
45A ASP* 3.8 1.0 + - - +
61A ARG 3.7 1.6 - - - +
62A VAL* 4.0 1.0 - - - -
63A THR* 2.8 59.2 + - + +
65A THR* 3.6 11.1 - - - +
463E THR* 4.2 13.2 - - + +
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Residues in contact with LEU 44 (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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42A LEU* 3.9 26.2 - - + -
43A ASP* 1.3 72.3 - - - +
45A ASP* 1.3 60.7 + - - +
46A THR* 5.4 0.4 - - - -
60A LEU* 4.8 5.2 - - + -
61A ARG 4.0 0.7 - - - -
62A VAL* 4.4 22.0 - - + -
107A PHE* 4.6 2.9 - - + -
131A VAL* 4.3 7.4 - - + -
133A PHE* 3.8 34.1 - - + -
459E ASP* 2.9 33.2 - - - +
460E LEU* 4.0 7.9 + - + +
462E TYR* 3.3 47.5 + - + +
463E THR* 3.7 13.1 - - - +
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Residues in contact with ASP 45 (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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43A ASP 3.8 2.0 + - - +
44A LEU* 1.3 73.2 - - - +
46A THR* 1.3 69.0 + - - +
47A ALA* 6.0 1.2 - - - +
60A LEU* 3.8 2.6 - - - +
61A ARG* 2.8 81.2 + - + +
63A THR* 5.3 0.7 - - - +
457E GLN 2.8 27.5 - - - +
458E THR* 3.5 7.7 - - - +
459E ASP* 3.1 13.9 + - + +
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Residues in contact with THR 46 (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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44A LEU 5.4 0.3 - - - -
45A ASP* 1.3 83.6 + - - +
47A ALA* 1.3 70.8 + - - +
58A VAL* 4.2 16.6 - - + -
59A VAL 3.6 8.7 - - - +
60A LEU* 3.5 17.2 - - - +
61A ARG* 6.0 0.2 - - - -
98A LEU 4.7 6.3 - - - +
99A GLY* 5.4 2.2 - - - -
103A PRO* 4.7 5.4 - - + +
456E ASP* 4.4 1.0 - - - +
457E GLN* 3.1 32.2 + - + +
459E ASP* 4.7 1.8 - - - +
460E LEU* 3.6 37.6 - - + +
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Residues in contact with ALA 47 (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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45A ASP* 6.0 1.1 - - - +
46A THR* 1.3 82.4 - - - +
48A SER* 1.3 60.8 + - - +
58A VAL* 3.7 4.7 - - - +
59A VAL* 2.9 49.5 + - + +
61A ARG* 6.3 2.0 - - + -
79A GLN* 5.1 6.7 - - - +
456E ASP* 3.4 20.2 - - + +
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Residues in contact with SER 48 (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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46A THR* 6.2 0.2 - - - -
47A ALA* 1.3 74.9 - - - +
49A SER* 1.3 60.3 + - - +
56A TYR* 3.0 40.5 + - - -
57A GLU 3.7 5.7 + - - -
58A VAL* 4.9 3.1 - - - +
59A VAL* 5.8 0.4 - - - -
98A LEU* 5.2 2.1 - - - +
454E LEU* 4.0 6.0 - - - +
455E THR* 3.6 27.3 - - - -
456E ASP* 3.1 21.6 + - - +
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Residues in contact with SER 49 (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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19A LYS* 4.7 3.8 + - - -
48A SER* 1.3 78.7 + - - +
50A GLN* 1.3 61.0 + - - +
51A LEU* 3.4 14.0 - - - +
56A TYR* 3.3 9.6 - - - -
57A GLU* 2.9 65.2 + - - +
59A VAL* 5.2 4.9 - - - -
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Residues in contact with GLN 50 (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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49A SER* 1.3 70.2 + - - +
51A LEU* 1.3 63.1 + - - +
52A ALA* 3.6 25.2 + - - +
53A ASP* 5.0 3.0 - - - +
56A TYR* 3.6 13.4 - - + -
30B HIS* 5.6 1.0 + - - -
452E VAL* 3.5 36.1 - - + +
453E GLY* 3.9 9.2 + - - -
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Residues in contact with LEU 51 (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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49A SER* 3.4 22.2 + - - +
50A GLN* 1.3 75.0 - - - +
52A ALA* 1.3 63.1 + - + +
55A VAL* 3.3 18.7 + - + +
57A GLU* 3.5 23.6 - - + +
83A ILE* 3.6 39.0 - - + -
29B PRO* 3.6 31.6 - - + +
30B HIS* 3.8 30.9 + - + +
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Residues in contact with ALA 52 (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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50A GLN* 3.6 20.5 - - - +
51A LEU* 1.3 78.0 - - - +
53A ASP* 1.3 71.5 + - - +
54A ASP 3.3 1.6 + - - -
55A VAL* 3.0 42.6 + - + +
452E VAL* 4.1 2.3 - - - +
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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