Contacts of the helix formed by residues 97 - 104 (chain Q) in PDB entry 3H1I
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 ASN 97 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D PRO* 4.3 11.7 - - + +
78D GLY* 3.1 35.1 + - - -
95Q TYR* 3.2 9.6 + - - +
96Q PRO* 1.3 94.4 + - - +
98Q PRO* 1.3 75.7 - - + +
99Q GLU* 3.4 11.3 + - - +
100Q ALA* 2.9 35.8 + - - +
101Q ALA* 3.2 9.2 + - - -
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Residues in contact with PRO 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q ASN* 1.3 87.0 - - + +
99Q GLU* 1.3 81.2 + - - +
100Q ALA 2.7 1.9 + - - -
101Q ALA* 2.8 19.9 + - + +
102Q ARG* 2.9 18.4 + - + +
109Q LEU* 4.2 26.0 - - + +
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Residues in contact with GLU 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D PRO* 3.6 27.9 - - - +
75D ASP 3.3 26.2 - - - +
76D GLU* 3.1 24.4 - - - +
78D GLY* 3.9 2.0 - - - +
97Q ASN* 3.4 12.0 + - - +
98Q PRO* 1.3 90.8 - - - +
100Q ALA* 1.3 58.5 + - - +
102Q ARG* 3.7 15.3 - - - +
103Q ALA* 3.6 12.0 + - - +
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Residues in contact with ALA 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASN 4.0 18.6 - - - +
78D GLY* 4.1 0.7 - - - +
95Q TYR* 4.0 5.1 - - + -
96Q PRO* 4.5 16.4 - - + -
97Q ASN* 2.9 28.3 + - - +
98Q PRO 2.7 5.1 + - - -
99Q GLU* 1.3 72.3 - - - +
101Q ALA* 1.3 67.0 + - - +
102Q ARG 3.1 0.9 - - - -
103Q ALA* 3.2 13.4 + - - +
104Q ALA* 3.3 12.0 + - - +
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Residues in contact with ALA 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95Q TYR* 3.2 41.6 - - + -
97Q ASN 3.2 5.0 + - - +
98Q PRO* 2.8 12.7 + - + +
100Q ALA* 1.3 78.3 - - - +
102Q ARG* 1.3 64.2 + - - +
104Q ALA* 3.0 15.2 + - - +
105Q ASN* 3.3 14.9 + - - +
108Q ALA 4.2 2.0 - - - -
109Q LEU* 4.4 13.7 - - + -
110Q PRO* 4.5 8.3 - - + -
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Residues in contact with ARG 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLU 5.6 0.7 - - - +
98Q PRO* 2.9 16.9 + - - +
99Q GLU* 3.7 18.4 - - - +
101Q ALA* 1.3 76.6 - - - +
103Q ALA* 1.3 61.8 + - - +
105Q ASN 3.0 8.3 + - - -
106Q ASN 3.1 0.2 + - - -
107Q GLY* 2.5 67.5 + - - -
108Q ALA 3.3 11.9 - - - +
109Q LEU* 3.4 44.3 - - + +
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Residues in contact with ALA 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLU 4.7 7.6 + - - +
77D ASN* 4.8 15.7 - - + +
99Q GLU 3.6 9.0 + - - +
100Q ALA* 3.2 12.1 + - - +
102Q ARG* 1.3 78.7 - - - +
104Q ALA* 1.3 58.9 + - - +
105Q ASN 3.3 1.1 + - - -
106Q ASN* 4.1 4.7 + - - -
107Q GLY 4.8 1.3 - - - +
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Residues in contact with ALA 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95Q TYR* 3.5 33.2 - - + +
100Q ALA 3.3 4.4 + - - +
101Q ALA 3.0 2.4 + - - +
103Q ALA* 1.3 79.5 - - - +
105Q ASN* 1.3 66.3 + - - +
106Q ASN 3.8 0.7 - - - -
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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