Contacts of the helix formed by residues 96 - 105 (chain H) in PDB entry 3SWD
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 ALA 96 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30H PHE* 4.0 11.2 - - + -
33H LEU* 4.4 11.0 - - + -
56H LEU* 4.3 17.7 - - + -
60H LEU* 4.5 4.5 - - + -
82H ALA* 4.5 4.0 - - + -
93H SER 2.7 19.7 + - - +
95H TRP* 1.3 73.0 - - - +
97H LEU* 1.3 65.1 + - - +
99H PRO* 3.4 3.1 - - - +
100H LEU* 3.2 38.4 + - + +
109H VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H ILE* 3.1 25.4 + - + +
96H ALA* 1.3 79.6 - - - +
98H GLY* 1.3 66.2 + - - +
100H LEU* 3.3 2.7 + - - +
101H VAL* 3.1 21.4 + - - +
107H GLY* 3.5 33.7 - - - +
109H VAL* 3.6 19.0 - - + +
125H HIS* 6.0 3.8 - - + -
126H ILE* 5.5 4.9 - - + +
129H LEU* 3.8 24.7 - - + -
136H ILE* 5.0 2.7 - - + -
143H VAL* 3.6 31.0 - - + +
145H ALA* 3.8 14.1 - - + -
168H THR* 6.0 1.1 - - + -
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Residues in contact with GLY 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H ILE 4.7 0.6 + - - -
95H TRP 4.1 2.2 + - - -
97H LEU* 1.3 77.1 - - - +
99H PRO* 1.3 71.6 - - - +
101H VAL* 3.2 2.0 + - - +
102H ALA* 3.0 23.4 + - - +
129H LEU* 4.4 15.5 - - - +
168H THR* 4.5 14.0 + - - +
172H ALA* 4.2 22.0 - - - +
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Residues in contact with PRO 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H PHE 3.4 21.8 - - - +
31H ALA* 4.4 7.0 - - - -
33H LEU* 3.8 26.0 - - + -
34H LEU* 3.7 24.1 - - + +
95H TRP 3.1 24.7 - - - +
96H ALA 3.4 5.8 - - - +
98H GLY* 1.3 81.7 - - - +
100H LEU* 1.3 63.5 + - - +
102H ALA* 3.8 0.7 - - - +
103H ARG* 3.0 28.4 + - - +
104H PHE* 5.6 0.4 - - - -
168H THR* 5.7 2.0 - - - +
171H CYS* 4.6 13.7 - - + -
172H ALA* 5.2 0.9 - - - -
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU* 4.1 18.4 - - + -
60H LEU* 4.2 18.4 - - + -
77H VAL* 4.3 9.6 - - + -
80H PHE* 3.7 39.3 - - + +
81H CYS* 5.3 0.9 - - - -
82H ALA 5.6 0.2 - - - +
96H ALA* 3.2 26.0 + - + +
97H LEU* 3.8 3.6 - - - +
99H PRO* 1.3 78.6 - - - +
101H VAL* 1.3 56.8 + - - +
104H PHE* 2.8 54.4 + - + +
106H GLN 3.0 18.8 - - - +
107H GLY* 4.2 5.6 - - - -
108H GLN 5.1 0.9 - - - +
109H VAL* 5.4 2.7 - - + -
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Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H LEU* 3.1 18.3 + - + +
98H GLY* 4.0 2.7 - - - +
100H LEU* 1.3 73.3 - - - +
102H ALA* 1.3 66.0 + - - +
103H ARG 3.2 0.2 - - - -
105H GLY* 3.0 21.7 + - - +
106H GLN 3.6 20.9 - - - +
107H GLY* 3.9 2.7 - - - +
129H LEU* 5.2 5.8 - - + -
134H ALA* 4.4 11.2 - - + -
145H ALA* 3.3 30.3 - - + +
146H SER 4.5 3.4 - - - -
147H VAL* 3.7 28.2 - - + +
149H GLY 5.3 0.3 - - - +
151H LEU* 4.3 15.9 - - + +
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LEU* 4.2 11.4 - - + -
98H GLY 3.0 16.8 + - - +
99H PRO 3.8 2.9 - - - +
101H VAL* 1.3 77.8 - - - +
103H ARG* 1.3 58.5 + - - +
105H GLY 5.1 0.2 + - - -
150H ARG* 4.9 9.7 - - - +
151H LEU* 3.7 15.0 + - + +
172H ALA* 3.4 34.8 - - - +
175H LEU* 3.8 22.0 - - + +
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Residues in contact with ARG 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU 2.6 37.3 + - - -
34H LEU* 3.9 13.2 - - + -
35H ALA 3.4 14.6 + - - -
36H GLU* 3.9 29.5 + - - +
74H ALA* 3.1 30.5 + - - +
75H ARG* 3.7 14.8 + - - +
77H VAL* 4.5 0.8 - - - +
99H PRO 3.0 15.1 + - - +
102H ALA* 1.3 80.2 - - - +
104H PHE* 1.3 94.9 + - + +
105H GLY 3.5 0.9 - - - -
175H LEU* 3.6 18.2 - - + -
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Residues in contact with PHE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 4.5 3.6 - - + -
75H ARG 5.7 0.7 - - - -
77H VAL* 3.6 42.8 - - + -
80H PHE* 3.4 39.0 - + + -
99H PRO 5.4 0.2 - - - -
100H LEU* 2.8 31.5 + - + +
103H ARG* 1.3 125.5 - - + +
105H GLY* 1.3 57.1 + - - +
106H GLN* 3.1 14.8 + - + +
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Residues in contact with GLY 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H VAL* 3.0 22.6 + - - -
102H ALA 4.8 0.2 - - - -
103H ARG 3.5 1.4 - - - -
104H PHE* 1.3 76.1 - - - +
106H GLN* 1.3 59.0 + - - +
146H SER* 3.3 5.9 - - - -
147H VAL* 2.9 47.4 + - - +
149H GLY 4.6 4.9 - - - -
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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