Contacts of the helix formed by residues 41 - 54 (chain C) in PDB entry 2HVY
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 TYR 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ASP* 3.2 1.2 + - - -
40C PRO* 1.3 105.1 - - + +
42C GLY* 1.3 58.6 + - - +
43C GLU 3.3 3.1 - - - +
44C TYR* 3.3 25.2 + + + +
45C ARG* 3.1 29.8 + - - +
38D ASN* 5.4 3.8 - - - -
41D THR* 3.4 30.0 - - + +
42D LYS* 3.0 23.6 + - - -
45D GLU* 2.9 40.3 + - - -
66D HIS* 3.9 34.0 - + + +
70D LEU* 4.6 5.8 - - + -
21E G 4.7 1.3 - - - -
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASP* 3.3 33.6 + - - -
40C PRO 3.5 0.8 - - - -
41C TYR* 1.3 74.7 - - - +
43C GLU* 1.3 59.5 + - - +
45C ARG* 3.4 14.5 + - - +
46C ARG* 3.0 43.9 + - - +
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A TYR* 4.0 14.9 - - - -
232A GLU* 4.4 9.8 - - - +
40C PRO 5.3 0.6 + - - +
41C TYR* 3.3 0.8 - - - +
42C GLY* 1.3 76.7 - - - +
44C TYR* 1.3 73.2 + - + +
46C ARG* 2.9 25.8 + - - +
47C ARG* 3.3 34.6 + - - +
50C ARG* 5.2 7.4 + - - -
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Residues in contact with TYR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PRO 5.0 3.6 - - - -
41C TYR* 3.3 34.2 + + - +
43C GLU* 1.3 82.0 - - + +
45C ARG* 1.3 65.2 + - - +
47C ARG* 3.4 31.0 + - - +
48C TRP* 3.4 11.4 + - - +
66D HIS* 3.7 23.2 - - + +
69D PRO* 3.2 27.9 - - + +
70D LEU* 3.8 45.1 - - + +
73D GLU* 4.2 15.4 - - + +
74D LYS* 5.1 7.3 + - - -
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A HIS* 3.6 31.7 + - - +
224A VAL* 3.5 12.3 - - - +
225A ASP* 2.7 40.4 + - - +
35C PHE* 4.9 0.2 - - - -
39C ASP* 2.8 43.0 + - - -
41C TYR 3.1 13.0 + - - +
42C GLY* 3.6 17.1 - - - +
44C TYR* 1.3 76.1 - - - +
46C ARG* 1.3 56.0 + - - +
48C TRP* 3.3 34.0 + - + -
49C LYS* 2.9 32.0 + - - +
62D GLU* 4.5 17.7 - - - +
65D ALA* 5.0 4.5 - - + -
66D HIS* 4.4 11.3 - - + +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 4.6 3.4 - - - +
225A ASP* 3.1 30.0 + - - +
228A TYR* 3.3 58.6 + - - +
229A PHE* 4.2 9.9 - - + -
232A GLU* 5.0 0.2 - - - -
39C ASP* 3.7 20.6 + - - +
42C GLY* 3.0 35.5 + - - +
43C GLU* 2.9 35.9 + - - +
44C TYR 3.3 0.4 - - - -
45C ARG* 1.3 76.0 - - - +
47C ARG* 1.3 55.2 + - - +
49C LYS* 3.7 6.2 - - - +
50C ARG* 2.7 62.1 + - - +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLU* 3.3 25.0 + - - +
44C TYR* 3.6 27.4 - - - +
45C ARG 3.3 0.2 - - - -
46C ARG* 1.3 77.6 - - + +
48C TRP* 1.3 62.0 - - - +
50C ARG* 4.0 10.0 - - - +
51C GLU* 3.2 22.9 + - - +
69D PRO* 4.2 22.1 + - + -
73D GLU* 2.6 41.2 + - - +
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Residues in contact with TRP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C TYR 3.4 8.9 + - - +
45C ARG* 3.3 40.1 + - + +
47C ARG* 1.3 79.6 - - - +
49C LYS* 1.3 77.9 + - + +
51C GLU* 3.3 11.6 + - - +
52C VAL* 3.1 44.8 + - + +
6D SER* 3.2 38.9 + - - -
7D TYR* 3.8 7.1 - - + +
9D LYS* 3.7 23.8 - - - +
61D GLU* 3.9 18.8 - - + -
62D GLU* 4.5 18.4 - - + -
65D ALA* 3.6 41.1 - - + +
69D PRO* 4.8 3.0 - - + +
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A HIS* 3.9 11.3 + - - +
222A ASP* 2.7 30.3 + - - +
225A ASP* 2.8 39.7 + - + +
226A TYR* 4.7 4.7 - - + -
229A PHE* 4.0 15.5 - - + -
45C ARG* 2.9 22.7 + - - +
46C ARG* 3.3 8.0 + - - +
48C TRP* 1.3 98.7 - - + +
50C ARG* 1.3 59.5 + - - +
52C VAL* 3.3 6.0 + - + +
53C LEU* 2.9 46.5 + - + +
62D GLU* 5.6 2.2 - - - +
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Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A TYR 4.3 3.2 + - - -
229A PHE* 3.6 24.9 - - + -
232A GLU* 3.2 24.9 + - - +
233A ASP* 2.9 37.7 + - - -
43C GLU* 5.2 6.5 + - - -
46C ARG* 2.7 51.2 + - - +
47C ARG* 4.0 9.4 - - - +
49C LYS* 1.3 70.8 - - - +
51C GLU* 1.3 59.9 + - - +
53C LEU 4.6 0.2 - - - +
54C GLY* 2.9 8.0 + - - -
55C ILE* 2.7 59.9 + - + -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ARG 3.2 15.0 + - - +
48C TRP* 3.4 15.9 - - - +
50C ARG* 1.3 78.0 - - - +
52C VAL* 1.3 64.7 + - - +
54C GLY* 3.5 8.2 + - - -
6D SER 4.5 4.4 - - - +
9D LYS* 3.4 41.4 + - - +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C TRP* 3.1 43.3 + - + +
49C LYS* 3.3 7.2 + - + +
51C GLU* 1.3 82.2 - - - +
53C LEU* 1.3 70.1 + - + +
54C GLY* 3.4 1.0 + - - -
6D SER* 3.8 22.4 - - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TYR* 4.2 13.5 - - + +
229A PHE* 3.7 30.1 - - + -
238A TYR* 3.9 37.2 + - + +
49C LYS* 2.9 29.6 + - + +
52C VAL* 1.3 83.8 - - + +
54C GLY* 1.3 62.0 + - - +
55C ILE* 3.9 18.2 - - + +
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG 2.9 6.3 + - - -
51C GLU 3.5 6.5 + - - -
52C VAL 3.2 4.8 + - - -
53C LEU* 1.3 80.5 - - - +
55C ILE* 1.3 62.9 + - - +
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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