Contacts of the helix formed by residues 37 - 55 (chain A) in PDB entry 1P39
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 GLN 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 4.2 0.9 - - - +
32A LYS* 3.9 23.1 - - + +
33A LYS* 3.0 52.4 - - - +
34A LEU* 3.0 33.5 + - + +
35A PRO 3.0 4.4 + - - -
36A TYR* 1.3 77.2 - - - +
38A GLY* 1.3 57.0 + - - +
40A LEU* 3.2 7.7 + - + +
41A LYS* 2.8 27.9 + - - +
200A PHE* 3.0 36.6 - - + +
201A ALA 3.4 13.7 - - - +
202A PRO* 4.5 0.7 - - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 5.1 2.2 - - - +
36A TYR* 3.1 1.4 - - - +
37A GLN* 1.3 76.5 - - - +
39A GLN* 1.3 64.7 + - - +
41A LYS* 3.6 13.3 - - - +
42A LEU* 3.1 32.1 + - - +
200A PHE 5.3 0.4 - - - -
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.0 21.2 + - + +
38A GLY* 1.3 74.1 - - - +
40A LEU* 1.3 56.6 + - - +
42A LEU* 3.4 2.9 + - - +
43A LEU* 2.8 36.0 + - - +
71A PRO* 4.1 12.7 - - - +
73A THR* 3.6 17.8 + - + -
74A HIS* 2.6 49.9 + - - +
294A LEU* 3.8 21.8 - - + -
400A SAH 2.9 26.3 + - - -
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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
----------------------------------------------------------
34A LEU* 3.8 23.3 - - + -
36A TYR 3.2 10.0 + - - +
37A GLN* 3.3 9.6 - - + +
39A GLN* 1.3 75.4 - - - +
41A LYS* 1.3 66.6 + - - +
43A LEU* 3.7 1.7 - - + +
44A LEU* 3.0 50.2 + - + +
200A PHE* 3.7 26.9 - - + -
263A MET* 4.9 0.2 - - - -
290A ILE* 3.7 28.7 - - + -
291A PHE* 3.8 23.6 - - + -
294A LEU* 3.7 13.8 - - + +
296A ILE* 4.0 7.2 - - + -
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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
----------------------------------------------------------
37A GLN 2.8 19.3 + - - +
38A GLY* 3.6 11.0 - - - +
39A GLN 3.3 0.2 - - - -
40A LEU* 1.3 74.8 - - - +
42A LEU* 1.3 84.2 + - - +
44A LEU* 4.1 2.5 - - - +
45A GLY* 3.3 17.8 + - - -
175A LYS* 5.4 2.2 - - - +
198A GLN* 3.6 36.3 - - + +
199A PRO* 3.8 23.6 - - - +
200A PHE* 3.6 11.2 - - - +
201A ALA* 3.7 21.1 - - + -
202A PRO* 4.5 9.9 - - + +
207A GLU* 3.0 23.2 + - - +
209A ARG* 4.1 2.8 - - - +
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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
----------------------------------------------------------
38A GLY 3.1 18.6 + - - +
39A GLN* 3.8 5.2 - - - +
41A LYS* 1.3 86.6 - - - +
43A LEU* 1.3 66.0 + - - +
45A GLY* 3.5 0.6 + - - -
46A GLU* 3.0 42.5 + - + +
74A HIS* 3.5 18.4 - - + +
138A ASP* 3.8 18.8 - - - +
198A GLN* 4.9 0.9 - - - +
209A ARG* 3.7 31.4 - - - +
400A SAH 3.4 37.2 - - + +
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Residues in contact with LEU 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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39A GLN 2.8 21.3 + - - +
40A LEU* 3.2 5.4 + - - +
42A LEU* 1.3 74.3 - - - +
44A LEU* 1.3 58.0 + - + +
46A GLU 3.8 0.2 - - - -
47A LEU* 2.8 35.7 + - + +
74A HIS* 3.6 27.1 - - + +
77A TYR* 3.6 37.0 - - + -
78A LEU* 3.3 31.1 - - + +
290A ILE* 3.9 29.6 - - + -
294A LEU* 3.9 17.0 - - + -
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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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40A LEU* 3.0 30.4 + - + +
41A LYS 4.1 2.5 - - - +
43A LEU* 1.3 75.7 - - - +
45A GLY* 1.3 58.7 + - - +
47A LEU* 3.3 4.0 + - - +
48A PHE* 2.9 31.0 + - - +
199A PRO* 4.0 15.3 - - + +
200A PHE* 3.7 29.6 - - + -
263A MET* 3.9 26.0 - - + +
266A MET* 3.8 17.8 - - + +
267A LEU* 3.8 35.6 - - + +
290A ILE* 4.2 13.0 - - + -
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Residues in contact with GLY 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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41A LYS 3.3 12.3 + - - -
42A LEU* 4.0 2.0 - - - -
44A LEU* 1.3 77.6 - - - +
46A GLU* 1.3 59.4 + - - +
48A PHE* 3.4 3.3 - - - +
49A PHE* 2.9 29.0 + - - +
196A MET* 3.6 31.7 - - - +
198A GLN* 5.9 0.4 - - - -
209A ARG* 5.3 5.4 - - - -
211A LEU* 5.4 1.0 - - - +
266A MET* 3.9 4.8 - - - +
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Residues in contact with GLU 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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42A LEU* 3.0 26.2 + - + +
43A LEU 4.1 0.4 - - - +
45A GLY* 1.3 74.1 - - - +
47A LEU* 1.3 60.6 + - - +
49A PHE* 3.9 6.9 - - - +
50A LEU* 3.0 35.3 + - + +
66A TYR* 2.5 39.4 + - - -
74A HIS* 2.7 28.3 + - - -
78A LEU* 3.2 24.9 - - + +
136A ILE* 4.2 21.7 - - + +
138A ASP* 5.5 0.3 - - - +
173A SER* 5.3 5.8 - - - +
209A ARG* 5.6 1.2 + - - -
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Residues in contact with LEU 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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43A LEU* 2.8 19.6 + - + +
44A LEU* 3.7 4.9 - - - +
46A GLU* 1.3 74.5 - - - +
48A PHE* 1.3 62.4 + - - +
50A LEU* 4.2 1.5 - - - +
51A SER* 2.8 35.0 + - - +
77A TYR* 4.2 12.8 - - + +
78A LEU* 3.7 22.6 - - + +
81A HIS* 3.7 36.8 - - + +
82A PHE* 4.3 3.8 - - + -
267A LEU* 4.2 14.6 - - + -
270A VAL* 4.0 19.1 - - + -
286A LEU* 5.3 2.0 - - + -
290A ILE* 3.9 27.8 - - + -
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Residues in contact with PHE 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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11A MET* 3.7 28.0 - - + -
12A TYR* 3.4 28.5 - + - -
44A LEU 2.9 18.4 + - - +
45A GLY 3.4 4.3 - - - +
47A LEU* 1.3 79.3 - - - +
49A PHE* 1.3 63.3 + - - +
51A SER* 3.8 3.0 - - - -
52A LYS* 3.3 23.7 + - + +
55A ARG* 4.7 6.9 + - - -
196A MET* 3.5 31.9 - - + -
211A LEU* 4.4 7.6 - - + -
266A MET* 3.7 30.5 - - + -
269A THR* 3.4 35.7 - - + -
270A VAL* 5.4 0.7 - - - -
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Residues in contact with PHE 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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45A GLY 2.9 17.6 + - - +
46A GLU* 3.9 5.6 - - - +
48A PHE* 1.3 76.7 - - - +
50A LEU* 1.3 83.5 + - + +
52A LYS* 3.2 25.1 + - + +
53A LEU* 3.3 34.5 + - + +
134A ILE* 4.0 8.7 - - + -
136A ILE* 4.2 11.0 - - + -
171A ALA* 3.9 2.9 - - + -
172A SER* 3.5 39.3 - - - -
173A SER* 3.7 20.4 - - - -
211A LEU* 3.8 40.2 - - + -
212A SER 4.4 4.0 - - - -
213A ILE* 5.5 0.9 - - + -
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Residues in contact with LEU 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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46A GLU 3.0 23.6 + - - +
49A PHE* 1.3 97.6 - - + +
51A SER* 1.3 64.8 + - - +
53A LEU* 3.3 17.5 + - + +
54A GLN 3.0 17.7 + - - -
59A LEU* 3.6 24.9 - - + +
64A VAL* 4.9 4.3 - - + -
78A LEU* 4.2 12.8 - - + -
82A PHE* 3.6 25.6 - - + -
91A TRP* 3.9 27.8 - - + -
134A ILE* 4.3 9.2 - - + -
136A ILE* 4.3 13.5 - - + -
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Residues in contact with SER 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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47A LEU* 2.8 23.3 + - - +
48A PHE 3.8 4.3 - - - -
50A LEU* 1.3 75.2 - - - +
52A LYS* 1.3 56.6 + - - +
54A GLN* 3.3 7.3 + - - +
55A ARG* 2.9 28.1 + - - +
81A HIS* 4.9 0.2 + - - -
82A PHE* 4.0 12.4 - - - -
269A THR* 3.9 23.8 - - - -
270A VAL* 3.9 21.5 - - - +
271A TYR* 3.3 18.9 - - - -
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Residues in contact with LYS 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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12A TYR* 4.8 9.2 + - - +
48A PHE* 3.3 11.7 + - + +
49A PHE* 3.2 16.7 + - + +
50A LEU 3.2 0.2 - - - -
51A SER* 1.3 75.4 - - - +
53A LEU* 1.3 61.5 + - + +
55A ARG* 3.0 28.3 + - - +
56A HIS* 2.9 52.1 + - + +
194A ASN* 3.3 25.9 + - - -
211A LEU* 4.5 26.2 + - + +
213A ILE* 4.2 25.9 - - + +
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Residues in contact with LEU 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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49A PHE* 3.3 30.9 + - + +
50A LEU* 3.6 15.3 - - + +
52A LYS* 1.3 80.8 - - + +
54A GLN* 1.3 58.3 + - - +
56A HIS* 3.2 2.3 + - - +
57A GLY 3.0 5.0 + - - -
58A ILE* 2.8 55.2 + - + +
59A LEU* 4.0 8.3 - - + -
134A ILE* 3.6 43.7 - - + -
171A ALA* 3.6 23.3 - - + -
213A ILE* 3.9 15.3 - - + -
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Residues in contact with GLN 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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50A LEU 3.0 13.2 + - - +
51A SER* 3.4 8.2 - - - +
53A LEU* 1.3 76.9 - - - +
55A ARG* 1.3 58.8 + - - +
57A GLY* 2.9 20.1 + - - +
59A LEU* 3.8 21.3 - - + +
60A ASP 6.1 0.2 - - - +
82A PHE* 3.2 24.9 - - - -
85A LEU* 4.1 12.0 - - - +
87A VAL* 4.3 17.8 - - + +
271A TYR* 3.3 40.2 - - + +
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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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48A PHE* 4.7 7.9 + - - -
51A SER* 2.9 16.2 + - - +
52A LYS* 3.1 42.8 + - - +
54A GLN* 1.3 78.1 - - - +
56A HIS* 1.3 66.5 + - + +
57A GLY 3.2 0.9 + - - -
269A THR* 3.3 37.7 + - - +
271A TYR* 3.0 34.0 + - - +
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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
------------------------------------------------------------
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