Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 4JHN
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 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 6.1 0.4 - - - -
14A VAL* 3.5 31.2 - - + -
31A TRP* 6.3 1.1 - - + -
32A PHE* 3.9 17.7 - - + -
35A ASP 4.7 0.4 - - - +
36A VAL* 1.3 98.4 - - + +
38A VAL* 1.3 62.6 + - - +
40A LEU* 4.5 4.5 - - + -
49A VAL* 4.0 14.8 - - + -
50A VAL 3.6 6.7 - - - +
51A THR* 4.2 1.8 - - + -
353A LEU* 4.1 7.7 - - + +
364A PHE* 3.7 40.0 - - + -
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Residues in contact with VAL 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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36A VAL* 3.6 6.0 + - + +
37A PRO* 1.3 78.8 - - - +
39A HIS* 1.3 65.0 + - + +
50A VAL* 2.8 27.7 + - + +
51A THR 3.6 15.7 - - - +
52A GLY* 3.7 21.8 - - - +
90A LYS* 4.9 6.1 - - - +
353A LEU* 3.5 20.6 - - - +
242C PRO* 3.8 24.5 - - + -
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Residues in contact with HIS 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 VAL* 1.3 83.6 - - + +
40A LEU* 1.3 82.8 + - - +
41A SER* 4.5 1.7 + - - -
48A ALA 4.0 0.2 - - - +
49A VAL* 3.6 4.7 - - - -
50A VAL* 2.9 45.5 + - + +
90A LYS 4.3 7.0 - - - +
91A LEU* 4.0 22.6 - - + +
92A ALA* 3.0 39.5 + - - +
144A GLN* 6.4 0.2 - - - +
145A LEU* 5.8 2.4 + - + -
353A LEU* 3.7 6.3 - - + +
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Residues in contact with LEU 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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14A VAL* 4.8 5.4 - - + -
37A PRO* 4.5 10.3 - - + -
39A HIS* 1.3 98.2 + - - +
41A SER* 1.3 62.6 + - - +
48A ALA 3.6 2.0 - - - +
49A VAL* 3.8 29.6 - - + -
299A TYR* 5.5 2.1 + - - -
353A LEU* 3.7 35.2 - - + +
354A VAL 4.1 3.3 - - - +
355A ALA* 3.8 18.2 - - + +
362A VAL* 3.6 40.2 - - + +
364A PHE* 3.7 16.4 - - + +
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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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39A HIS* 4.5 1.6 - - - -
40A LEU* 1.3 76.4 - - - +
42A CYS* 1.3 68.9 + - - +
47A SER* 3.4 2.6 - - - -
48A ALA* 2.8 38.8 + - - +
92A ALA 3.5 21.3 - - - -
93A ALA* 3.3 4.6 - - - +
94A CYS* 2.9 35.6 + - - +
355A ALA* 3.8 3.4 - - - -
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Residues in contact with CYS 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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41A SER* 1.3 79.7 + - - +
43A GLY* 1.3 60.3 + - - +
46A HIS 3.5 4.3 - - - -
47A SER* 3.7 8.3 - - - -
94A CYS* 3.6 11.2 - - - +
355A ALA* 3.6 26.6 - - - +
356A CYS 3.6 14.8 + - - +
357A GLY* 3.5 21.7 - - - +
360A HIS* 3.7 11.2 - - - +
362A VAL* 3.5 33.0 - - - -
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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