Contacts of the helix formed by residues 35 - 41 (chain A) in PDB entry 1P4D
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 GLY 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 1.3 76.4 - - - +
36A ARG* 1.3 66.5 + - - -
37A GLY 3.1 3.4 - - - -
38A ALA* 3.1 11.1 + - - +
39A GLU* 3.2 13.1 + - - +
44A GLN* 5.8 0.7 + - - -
118A GLU* 3.4 14.1 - - - -
139A LEU 3.4 6.5 - - - -
141A MET* 3.8 12.4 - - - +
612A EDO 4.3 8.1 + - - -
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Residues in contact with ARG 36 (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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35A GLY* 1.3 70.3 - - - -
37A GLY* 1.3 56.1 + - - +
39A GLU* 3.3 14.2 + - - +
40A GLN* 3.0 25.7 + - - +
115A ARG* 5.5 8.1 + - - +
118A GLU* 2.6 37.7 + - - +
119A ALA* 5.4 0.2 - - - +
137A GLY* 2.9 19.1 + - - +
138A ASN* 3.7 14.8 - - + -
101B ARG* 4.5 12.2 - - - +
211B LEU 5.2 0.4 + - - -
292B ARG* 6.3 0.7 - - - +
296B ASP* 2.8 56.5 + - + +
299B ALA* 4.6 7.9 - - - +
300B ASP* 2.6 45.4 + - - -
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Residues in contact with GLY 37 (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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36A ARG* 1.3 77.1 - - - +
38A ALA* 1.3 64.0 + - - -
40A GLN* 3.0 15.9 + - - +
41A LEU* 3.1 17.7 + - - +
138A ASN* 3.9 8.7 - - - +
139A LEU 2.9 17.6 + - - +
140A VAL* 3.6 15.0 - - - -
172A TRP* 3.9 11.9 - - - -
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Residues in contact with ALA 38 (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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33A TRP* 4.0 13.5 - - + -
34A ALA 3.4 25.4 - - - +
35A GLY 3.1 4.2 + - - +
37A GLY* 1.3 75.5 - - - +
39A GLU* 1.3 57.0 + - - +
41A LEU* 3.2 2.0 + - - -
42A GLY 3.2 3.6 + - - -
43A LEU* 2.7 52.8 + - + +
44A GLN* 5.2 1.3 - - - +
139A LEU 3.4 4.6 + - - -
140A VAL* 3.7 19.8 - - + +
141A MET 4.5 0.4 - - - +
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Residues in contact with GLU 39 (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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35A GLY 3.2 8.4 + - - +
36A ARG* 3.4 15.8 - - - +
37A GLY 3.1 0.2 - - - -
38A ALA* 1.3 80.3 - - - +
40A GLN* 1.3 61.3 + - - +
42A GLY* 3.0 13.7 + - - +
43A LEU 4.1 6.9 + - - +
44A GLN* 3.3 27.1 - - + +
98B GLY 3.9 7.4 - - - +
99B ASP* 5.0 1.1 - - - +
100B LYS 5.9 0.4 - - - -
101B ARG* 4.9 11.1 + - - +
292B ARG* 2.5 47.8 + - - -
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Residues in contact with GLN 40 (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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36A ARG 3.0 12.2 + - - +
37A GLY* 3.0 14.2 + - - +
39A GLU* 1.3 77.5 - - - +
41A LEU* 1.3 58.9 + - + +
42A GLY 3.2 0.6 + - - -
167A GLN* 3.2 31.4 + - - +
172A TRP* 4.3 7.6 - - + -
289B ARG* 5.6 5.5 + - - +
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Residues in contact with LEU 41 (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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37A GLY 3.1 11.1 + - - +
38A ALA 3.2 6.5 + - - +
39A GLU 3.2 0.4 - - - -
40A GLN* 1.3 77.2 - - + +
42A GLY* 1.3 62.8 + - - +
43A LEU* 3.5 17.5 + - + +
55A LEU* 4.8 3.6 - - + -
60A LEU* 4.3 10.1 - - + -
61A PRO* 3.7 41.1 - - + +
62A ASP* 3.8 35.2 - - + +
140A VAL* 4.2 15.3 - - + -
172A TRP* 3.4 34.5 - - + +
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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