Contacts of the helix formed by residues 52 - 61 (chain A) in PDB entry 3AE1
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 PHE 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 1.3 72.9 - - - +
53A PRO* 1.3 69.2 - - + +
54A THR* 3.6 32.1 - - - -
55A ARG* 2.6 51.2 + - + +
56A SER 3.6 2.1 + - - -
163A TYR* 3.2 35.2 - + - -
175A VAL* 3.8 21.9 - - + +
176A GLU* 4.4 11.4 + - - +
119B TYR* 3.3 67.8 - + + +
122B TYR* 6.0 0.7 - + - -
160B LEU* 5.3 6.7 - - + -
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Residues in contact with PRO 53 (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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27A ALA* 3.3 33.3 - - + +
32A LEU* 4.3 5.8 - - + -
49A THR* 4.3 4.3 - - + -
51A LEU 3.5 6.0 - - - +
52A PHE* 1.3 93.2 - - + -
54A THR* 1.3 60.2 + - - +
56A SER* 2.7 25.3 + - - +
159A LEU* 3.4 7.9 - - - +
163A TYR* 3.6 38.4 - - + -
173A TYR* 4.7 15.5 - - + -
175A VAL* 3.9 11.4 - - + -
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Residues in contact with THR 54 (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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52A PHE* 2.9 25.0 + - + -
53A PRO* 1.3 77.9 - - - +
55A ARG* 1.3 65.3 + - - +
59A VAL* 2.9 32.1 - - + +
159A LEU* 3.3 9.4 - - - +
160A HIS* 3.4 43.7 + - + +
163A TYR* 4.2 15.3 - - - +
70B CYS 4.1 8.2 - - - +
159B ILE* 4.0 15.3 - - + +
160B LEU* 4.4 4.8 - - + +
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Residues in contact with ARG 55 (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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51A LEU* 3.9 16.1 - - + +
52A PHE* 2.6 38.6 + - + +
54A THR* 1.3 73.4 - - - +
56A SER* 1.3 65.6 + - - +
57A HIS* 3.6 1.0 + - - -
59A VAL* 4.0 0.2 - - - +
62B ARG* 6.2 1.8 - - - +
64B SER* 4.0 11.8 + - - -
70B CYS* 2.8 52.8 + - + +
71B GLY* 3.2 21.4 + - - -
72B SER* 3.6 28.4 + - - +
115B LEU* 4.3 10.5 - - - +
118B PHE* 5.3 0.4 - - - -
119B TYR* 3.1 34.0 + - - -
159B ILE 3.4 9.1 + - - -
160B LEU* 2.8 29.8 + - - +
161B CYS* 4.4 2.6 + - - +
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Residues in contact with SER 56 (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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27A ALA 3.2 5.2 + - - -
28A GLY* 3.6 21.8 - - - -
51A LEU* 4.0 12.3 - - - +
52A PHE 3.6 2.8 + - - -
53A PRO* 2.7 25.0 + - - +
54A THR 3.2 1.0 - - - -
55A ARG* 1.3 81.6 - - - +
57A HIS* 1.3 59.7 - - - +
58A THR 2.9 8.2 + - - -
59A VAL* 2.9 17.5 + - - +
159A LEU* 3.5 5.1 - - - +
700A FAD 2.8 29.1 + - - -
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Residues in contact with HIS 57 (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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51A LEU* 4.9 3.2 - - - +
55A ARG 3.6 2.4 + - - -
56A SER* 1.3 71.8 - - - +
58A THR* 1.3 63.0 + - - +
59A VAL* 3.0 2.7 - - - -
60A ALA* 3.0 26.4 + - + +
61A ALA 4.1 1.4 + - - -
225A THR 3.6 2.2 - - - -
226A SER* 3.6 3.1 - - - -
227A ALA* 3.4 39.3 + - + +
229A THR* 5.3 3.0 + - - +
230A SER* 4.3 14.4 - - - +
398A GLU* 5.1 4.5 - - - -
700A FAD 1.9 98.6 + + + +
65B CYS* 5.7 2.3 - - - +
67B GLU* 5.3 0.7 - - - -
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Residues in contact with THR 58 (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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29A GLY* 3.1 28.3 + - - +
56A SER 2.9 0.8 + - - -
57A HIS* 1.3 78.5 - - - +
59A VAL* 1.3 60.5 + - - +
61A ALA* 3.3 8.0 + - - +
155A GLY* 3.0 28.8 - - - +
158A LEU* 4.6 3.6 - - + -
159A LEU* 3.9 21.1 - - + +
415A LEU* 3.9 19.7 - - + -
418A LEU* 3.7 2.0 - - + +
700A FAD 2.7 39.1 + - - -
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Residues in contact with VAL 59 (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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54A THR 2.9 25.1 - - - +
55A ARG 4.0 2.9 - - - +
56A SER 2.9 18.8 + - - +
57A HIS* 4.3 2.2 - - - -
58A THR* 1.3 78.0 - - - +
60A ALA* 1.3 63.8 + - - +
61A ALA 3.1 3.2 + - - +
156A HIS* 3.2 52.8 + - + +
159A LEU* 3.6 12.1 - - + +
160A HIS* 4.3 7.4 - - + +
65B CYS* 5.7 0.4 - - + -
69B ILE* 4.5 12.4 - - + +
70B CYS* 3.8 30.1 - - + +
159B ILE* 4.4 4.5 - - + -
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Residues in contact with ALA 60 (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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57A HIS* 3.0 23.8 + - + +
59A VAL* 1.3 79.0 - - + +
61A ALA* 1.3 63.5 + - - +
62A GLN* 3.5 22.7 + - - +
700A FAD 3.5 26.5 - - + -
65B CYS* 5.4 1.3 - - + -
67B GLU* 3.9 9.8 - - - +
69B ILE* 3.7 25.8 - - + -
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Residues in contact with ALA 61 (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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57A HIS 4.1 0.6 + - - -
58A THR* 3.3 8.8 + - - +
59A VAL 3.1 5.3 - - - +
60A ALA* 1.3 79.7 - - - +
62A GLN* 1.3 58.4 + - - +
153A ARG* 3.9 3.1 - - - -
154A THR 3.8 2.6 + - - -
155A GLY* 2.9 40.8 + - - +
156A HIS 3.7 1.2 + - - -
415A LEU* 3.8 10.8 - - + -
700A FAD 3.0 41.5 - - + +
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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