Contacts of the helix formed by residues 96 - 105 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30L PHE* 4.0 11.5 - - + -
33L LEU* 4.4 11.0 - - + -
56L LEU* 4.3 17.7 - - + -
60L LEU* 4.6 3.4 - - + -
82L ALA* 4.5 4.7 - - + -
93L SER 2.7 18.7 + - - +
95L TRP* 1.3 71.1 - - - +
97L LEU* 1.3 67.9 + - - +
99L PRO* 3.3 4.0 - - - +
100L LEU* 3.1 37.7 + - + +
109L VAL* 4.2 10.8 - - + -
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Residues in contact with LEU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ILE* 3.1 24.8 + - + +
96L ALA* 1.3 79.5 - - - +
98L GLY* 1.3 66.8 + - - +
100L LEU* 3.4 2.7 + - - +
101L VAL* 3.2 20.3 + - - +
107L GLY* 3.5 33.4 - - - +
109L VAL* 3.5 19.6 - - + +
125L HIS* 6.0 4.0 - - + -
126L ILE* 5.5 4.3 - - + +
129L LEU* 3.7 25.8 - - + -
136L ILE* 5.0 2.7 - - + -
143L VAL* 3.6 31.6 - - + +
145L ALA* 3.9 13.7 - - + -
168L THR* 6.0 1.3 - - + -
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Residues in contact with GLY 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ILE 4.7 0.8 + - - -
95L TRP 4.1 2.0 + - - -
97L LEU* 1.3 79.2 - - - +
99L PRO* 1.3 71.6 - - - +
101L VAL* 3.2 1.4 + - - +
102L ALA* 3.0 23.7 + - - +
129L LEU* 4.5 14.0 - - - +
168L THR* 4.5 14.6 + - - +
172L ALA* 4.2 21.3 - - - +
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Residues in contact with PRO 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L PHE 3.4 29.2 - - - +
31L ALA* 4.4 6.3 - - - -
33L LEU* 3.8 18.6 - - + -
34L LEU* 3.7 23.7 - - + +
95L TRP 3.1 23.6 - - - +
96L ALA 3.3 5.4 - - - +
98L GLY* 1.3 82.5 - - - +
100L LEU* 1.3 63.1 + - - +
102L ALA* 3.3 1.3 + - + +
103L ARG* 3.0 28.1 + - - +
104L PHE* 5.6 0.4 - - - -
168L THR* 5.7 1.3 - - - +
171L CYS* 4.6 13.7 - - + -
172L ALA* 5.6 0.7 - - - -
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Residues in contact with LEU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L LEU* 4.2 18.6 - - + -
60L LEU* 4.2 17.7 - - + -
77L VAL* 4.3 10.1 - - + -
79L VAL 4.8 0.4 - - - +
80L PHE* 3.7 39.7 - - + +
81L CYS* 5.2 1.6 - - - -
96L ALA* 3.1 27.0 + - + +
97L LEU* 3.8 3.8 - - - +
99L PRO* 1.3 79.7 - - - +
101L VAL* 1.3 58.0 + - - +
104L PHE* 2.8 53.1 + - + +
106L GLN 3.0 19.4 - - - +
107L GLY* 4.2 4.9 - - - -
108L GLN 5.2 0.9 - - - +
109L VAL* 5.4 2.5 - - + -
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Residues in contact with VAL 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L LEU* 3.2 17.6 + - + +
98L GLY* 4.0 2.9 - - - +
100L LEU* 1.3 73.2 - - - +
102L ALA* 1.3 67.9 + - - +
105L GLY* 3.1 21.5 + - - +
106L GLN 3.6 19.7 - - - +
107L GLY* 3.9 3.4 - - - +
129L LEU* 5.2 6.1 - - + -
134L ALA* 4.5 11.0 - - + -
145L ALA* 3.3 30.3 - - + +
146L SER 4.6 2.9 - - - -
147L VAL* 3.8 28.2 - - + +
151L LEU* 4.3 16.1 - - + +
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Residues in contact with ALA 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L LEU* 4.2 12.1 - - + -
98L GLY 3.0 16.6 + - - +
99L PRO 3.8 2.9 - - - +
101L VAL* 1.3 78.0 - - - +
103L ARG* 1.3 59.8 + - - +
150L ARG* 4.9 9.5 - - - +
151L LEU* 3.8 14.3 + - + +
172L ALA* 3.5 34.5 - - - +
175L LEU* 3.9 22.7 - - + +
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Residues in contact with ARG 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L LEU 2.6 36.3 + - - -
34L LEU* 3.9 13.2 - - + -
35L ALA 3.4 14.2 + - - -
36L GLU* 3.8 30.1 + - - +
74L ALA* 3.1 30.9 + - - +
75L ARG* 3.7 15.8 + - - +
77L VAL* 4.5 0.6 - - - +
99L PRO 3.0 16.0 + - - +
102L ALA* 1.3 78.9 - - - +
104L PHE* 1.3 93.2 + - + +
105L GLY 3.6 0.2 - - - -
175L LEU* 3.6 18.4 - - + -
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Residues in contact with PHE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L LEU 4.5 3.4 - - - -
75L ARG 5.7 0.7 - - - -
77L VAL* 3.7 42.0 - - + -
80L PHE* 3.4 37.5 - + + -
99L PRO 5.9 0.2 - - - -
100L LEU* 2.8 31.1 + - + +
103L ARG* 1.3 124.4 - - + +
105L GLY* 1.3 57.9 + - - +
106L GLN* 3.1 15.2 + - + +
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Residues in contact with GLY 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L LEU 3.6 0.2 + - - -
101L VAL* 3.1 22.4 + - - -
102L ALA 5.1 0.2 + - - -
103L ARG 3.6 1.4 - - - -
104L PHE* 1.3 77.5 - - - +
106L GLN* 1.3 58.8 + - - +
146L SER* 3.3 5.4 - - - -
147L VAL* 2.9 46.3 + - - +
149L GLY 4.6 5.2 - - - -
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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