Contacts of the helix formed by residues 51 - 61 (chain D) in PDB entry 4F2N
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 SER 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D GLY* 3.9 0.9 - - - -
47D GLN* 4.3 4.0 - - - +
49D VAL 4.0 0.6 + - - -
50D MET* 1.3 75.3 - - - +
52D PRO* 1.3 75.4 - - - +
53D ARG* 3.8 6.5 + - - +
54D GLN 3.1 15.8 + - - -
55D LEU* 3.1 21.5 + - - +
199D LYS* 4.4 1.6 - - - +
200D ASP* 2.5 35.9 + - - -
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Residues in contact with PRO 52 (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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42D TYR 4.5 3.5 - - - +
43D LYS* 3.2 27.1 - - - +
44D ASP* 3.9 15.3 - - - +
45D GLY* 3.7 11.0 - - - +
47D GLN* 4.4 6.1 - - - +
51D SER* 1.3 86.3 - - - +
53D ARG* 1.3 52.3 + - - +
55D LEU* 3.3 2.1 + - - +
56D GLU* 2.8 36.8 + - - +
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Residues in contact with ARG 53 (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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202C GLU* 2.7 36.3 + - - +
51D SER* 3.3 5.9 + - - +
52D PRO* 1.3 76.2 - - - +
54D GLN* 1.3 67.8 + - - +
56D GLU* 3.1 34.0 + - - +
57D LEU* 2.9 46.3 + - + +
61D LYS* 5.5 6.9 - - - +
199D LYS* 3.4 29.4 - - - -
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Residues in contact with GLN 54 (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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198C TYR* 4.8 5.5 + - - -
50D MET* 4.4 14.4 - - + -
51D SER* 3.1 13.6 + - - +
53D ARG* 1.3 77.1 - - - +
55D LEU* 1.3 62.9 + - - +
57D LEU* 3.5 3.2 + - - +
58D HIS* 3.1 25.4 + - + +
195D HIS 2.9 23.6 + - - -
196D ALA* 3.3 17.2 + - - +
197D TYR* 3.2 16.0 - - - -
199D LYS* 3.1 40.0 + - + +
200D ASP* 3.2 32.2 + - + +
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Residues in contact with LEU 55 (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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38D LEU* 5.0 2.2 - - + -
40D PHE* 3.9 7.9 - - + -
42D TYR* 3.5 41.1 - - + +
45D GLY* 3.6 26.0 - - - +
46D ILE* 3.8 15.9 - - + -
50D MET* 4.6 9.6 - - + +
51D SER 3.1 16.1 + - - +
52D PRO 3.8 2.7 - - - +
54D GLN* 1.3 75.3 - - - +
56D GLU* 1.3 61.4 + - - +
58D HIS* 4.4 1.8 - - - -
59D TYR* 2.9 42.5 + - + +
112D TRP* 3.6 36.1 - - + -
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Residues in contact with GLU 56 (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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42D TYR* 4.5 20.0 + - + -
52D PRO 2.8 21.4 + - - +
53D ARG* 3.1 36.8 + - - +
55D LEU* 1.3 74.4 - - - +
57D LEU* 1.3 58.2 + - - +
60D SER* 2.8 52.0 + - - +
61D LYS* 3.6 6.8 + - + +
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Residues in contact with LEU 57 (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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198C TYR* 3.8 25.6 - - + +
202C GLU* 3.6 34.5 - - + +
203C ASN* 3.8 22.0 - - - +
53D ARG* 2.9 56.6 + - + +
54D GLN* 3.8 5.4 - - - +
56D GLU* 1.3 75.0 - - - +
58D HIS* 1.3 64.0 + - - +
61D LYS* 3.1 20.2 + - + +
62D HIS* 3.0 24.0 + - + -
199D LYS* 4.3 12.6 - - + -
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Residues in contact with HIS 58 (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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50D MET* 5.3 4.6 - - - +
54D GLN* 3.1 22.5 + - + +
55D LEU* 3.8 5.2 - - - +
57D LEU* 1.3 77.6 - - - +
59D TYR* 1.3 57.8 + - - +
62D HIS* 3.3 11.9 - - + +
63D HIS* 2.9 27.4 + - - +
108D HIS* 3.1 23.5 + + - -
111D PHE* 4.1 14.9 - + - -
112D TRP* 3.6 18.0 - + + -
191D ASP* 2.7 31.3 + - - -
195D HIS* 3.3 20.9 + + - +
196D ALA* 3.6 32.0 + - + -
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Residues in contact with TYR 59 (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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35D LEU* 3.6 39.0 + - + +
36D PRO* 2.5 31.7 + - + -
37D THR* 4.4 2.8 - - - -
38D LEU* 3.6 33.4 + - + +
42D TYR* 4.2 22.2 - + + -
55D LEU* 2.9 24.1 + - + +
58D HIS* 1.3 78.5 - - - +
60D SER* 1.3 70.7 + - - +
63D HIS* 3.4 5.1 - - - +
64D SER 3.1 25.1 + - - -
112D TRP* 3.7 31.2 - + + -
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Residues in contact with SER 60 (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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35D LEU* 5.0 2.9 - - - -
42D TYR* 3.5 31.5 + - - -
56D GLU* 2.8 27.6 + - - +
59D TYR* 1.3 79.5 - - - +
61D LYS* 1.3 68.9 + - - +
64D SER* 3.1 19.8 + - - -
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Residues in contact with LYS 61 (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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203C ASN* 3.6 39.7 - - + +
53D ARG* 5.5 8.1 - - - +
56D GLU* 4.3 7.6 - - + +
57D LEU* 3.1 28.3 + - + +
60D SER* 1.3 90.9 - - - +
62D HIS* 1.3 66.4 + - - +
63D HIS 3.6 0.4 - - - -
64D SER 4.1 0.2 - - - -
65D ALA* 3.1 25.3 + - - +
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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