Contacts of the helix formed by residues 25 - 37 (chain B) in PDB entry 2FHP
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 THR 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MSE 5.9 3.8 - - - -
26B ASP* 1.3 65.8 + - - +
27B LYS* 3.6 11.2 + - + +
28B VAL* 3.2 43.3 - - + +
29B LYS* 2.9 28.0 + - - +
150B GLU* 5.9 0.8 + - - -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B ALA 4.4 2.6 - - - +
1B MSE 3.6 22.0 - - - +
2B ARG* 2.8 37.5 + - - +
4B ILE* 3.7 15.9 - - + +
25B THR* 1.3 76.3 + - - +
27B LYS* 1.3 62.6 + - + +
29B LYS* 3.3 25.9 + - - +
30B GLU* 2.9 30.2 + - - +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 3.3 10.3 + - + +
26B ASP* 1.3 80.9 - - + +
28B VAL* 1.3 56.4 + - + +
30B GLU* 3.4 20.8 + - - +
31B SER* 3.0 32.9 + - - +
172B TYR* 6.2 0.7 - - - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 3.2 30.8 - - + +
27B LYS* 1.3 75.2 - - + +
29B LYS* 1.3 59.3 + - - +
31B SER* 3.2 6.9 + - - -
32B ILE* 2.8 45.1 + - + +
150B GLU* 4.2 9.0 - - - +
172B TYR* 3.8 19.7 - - + +
175B THR* 3.5 34.8 - - + -
177B VAL* 4.1 12.6 - - + -
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MSE 4.9 3.0 - - - +
2B ARG 2.9 26.0 + - - -
3B VAL* 4.4 0.2 - - - +
4B ILE* 3.8 8.3 - - - -
13B LEU* 3.7 20.0 - - - +
25B THR 2.9 15.3 + - - +
26B ASP* 3.3 22.3 + - - +
28B VAL* 1.3 77.1 - - - +
30B GLU* 1.3 62.6 + - - +
32B ILE* 3.4 8.6 + - - +
33B PHE* 3.1 39.6 + - + +
54B GLY* 4.0 21.1 + - - +
55B LEU* 3.8 23.8 - - + -
58B GLU* 3.8 22.5 + - + +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 35.3 - - + +
26B ASP 2.9 17.9 + - - +
27B LYS* 3.6 24.3 - - - +
29B LYS* 1.3 74.9 - - - +
31B SER* 1.3 58.0 + - - +
33B PHE* 3.3 0.9 + - - +
34B ASN* 3.0 55.5 + - - +
62B ARG* 4.5 4.3 - - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 3.0 19.3 + - - +
28B VAL* 3.4 6.7 - - - -
30B GLU* 1.3 75.4 - - - +
32B ILE* 1.3 66.0 + - - +
34B ASN* 4.0 4.1 - - - +
35B MSE 3.1 30.3 + - - +
172B TYR* 3.6 41.0 + - - -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 2.8 33.5 + - + +
29B LYS* 3.6 8.1 - - - +
31B SER* 1.3 73.7 - - - +
33B PHE* 1.3 79.6 + - + +
35B MSE 3.2 21.7 + - - +
36B ILE* 3.2 15.3 + - + +
55B LEU* 4.7 9.0 - - + -
118B LEU* 5.0 1.1 - - + -
148B VAL* 3.7 37.2 - - + -
150B GLU* 4.0 31.2 - - + +
177B VAL* 3.8 23.8 - - + -
179B ILE* 5.1 1.3 - - + -
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS* 3.1 28.7 + - + +
32B ILE* 1.3 87.0 - - + +
34B ASN* 1.3 58.4 + - - +
36B ILE* 3.9 7.1 - - + +
37B GLY* 2.9 26.0 + - - -
38B PRO* 3.4 7.6 - - - +
40B PHE* 3.8 18.8 - + - -
55B LEU* 3.5 39.7 - - + -
58B GLU* 3.5 23.6 - - + -
59B ALA* 3.7 25.6 - - + -
62B ARG* 3.4 37.9 - - - +
116B LEU* 4.1 9.0 - - + -
118B LEU* 4.1 16.2 - - + -
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B SER* 5.2 1.0 + - - -
30B GLU* 3.0 40.9 + - - +
31B SER* 4.2 4.0 - - - +
33B PHE* 1.3 75.6 - - - +
35B MSE 1.3 62.2 + - - +
37B GLY 4.1 1.0 + - - +
38B PRO* 3.7 26.5 - - + +
62B ARG* 3.2 23.0 + - - +
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Residues in contact with MSE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER 3.1 18.8 + - - +
32B ILE* 3.2 16.8 + - - +
34B ASN* 1.3 79.3 - - - +
36B ILE* 1.3 63.3 + - + +
37B GLY 4.6 2.1 - - - +
168B ARG* 3.2 56.0 + - + +
170B THR* 4.5 12.1 - - - +
172B TYR* 3.9 27.8 - - + +
177B VAL* 3.7 31.6 - - + +
179B ILE* 4.3 6.7 - - + -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.4 15.3 - - + +
33B PHE* 3.9 19.1 - - + +
35B MSE 1.3 77.1 - - + +
37B GLY* 1.3 63.6 + - - +
40B PHE* 3.8 27.8 - - + -
116B LEU* 3.7 30.3 - - + -
146B VAL* 3.7 25.8 - - + +
148B VAL* 3.8 10.8 - - + -
168B ARG* 5.1 0.4 - - - +
179B ILE* 3.7 32.8 - - + -
181B ARG* 3.4 23.1 + - - +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PHE 2.9 10.5 + - - -
34B ASN 4.1 3.6 - - - +
35B MSE 4.6 1.9 - - - +
36B ILE* 1.3 82.5 - - - +
38B PRO* 1.3 73.3 - - - +
39B TYR 3.3 14.4 - - - -
40B PHE* 4.0 9.0 - - - -
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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