Contacts of the helix formed by residues 103 - 116 (chain C) in PDB entry 3SDL
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 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C HIS* 6.0 4.0 - - + -
101C THR 5.2 2.5 - - - +
102C GLN* 1.3 81.6 - - - +
104C VAL* 1.3 64.2 + - - +
105C ALA* 3.5 6.9 + - - +
106C HIS* 3.0 34.2 + - - +
107C LEU* 3.2 10.2 + - - +
133C ASP 3.6 12.1 - - - +
134C GLN* 4.2 15.0 - - - +
135C LEU 3.4 7.6 - - - +
136C PRO* 4.1 2.5 - - + -
137C LEU* 4.4 1.9 - - - +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN 4.0 0.2 + - - -
103C THR* 1.3 72.5 - - - +
105C ALA* 1.3 56.5 + - - +
107C LEU* 3.2 3.6 + - - +
108C LYS* 3.0 34.7 + - + +
124C LEU* 4.7 5.4 - - + -
131C LEU* 3.6 32.3 - - + +
132C GLU 3.0 34.5 - - - +
133C ASP* 3.5 6.7 + - - +
135C LEU 2.8 19.4 + - - +
137C LEU* 4.0 18.6 - - + +
140C TYR* 3.7 24.0 - - + -
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C THR* 3.0 7.6 - - - +
104C VAL* 1.3 79.0 - - - +
106C HIS* 1.3 56.1 + - - +
108C LYS* 3.3 9.0 + - - +
109C GLN* 3.1 39.6 + - - +
119C ASP* 5.5 0.7 - - - +
133C ASP* 3.1 36.8 + - + +
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Residues in contact with HIS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 2.9 37.5 + - + +
103C THR* 3.0 27.0 + - - +
105C ALA* 1.3 74.2 - - - +
107C LEU* 1.3 63.0 + - - +
109C GLN* 3.3 25.2 + - + +
110C GLN* 3.2 47.8 + - + +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE* 3.8 24.0 - - + -
86C VAL* 4.4 6.3 - - + -
96C TYR* 4.3 13.5 - - + -
98C VAL* 3.9 21.3 - - + -
102C GLN* 4.1 5.6 - - - +
103C THR 3.2 10.5 + - - +
104C VAL 3.2 7.6 + - - +
106C HIS* 1.3 77.7 + - - +
108C LYS* 1.3 56.6 + - - +
110C GLN* 3.1 7.7 + - + +
111C VAL* 2.9 42.1 + - + +
124C LEU* 3.7 24.2 - - + -
131C LEU* 4.8 5.4 - - + -
137C LEU* 3.7 31.9 - - + -
148C VAL* 5.0 2.9 - - + -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.0 19.7 + - + +
105C ALA* 3.6 9.9 - - - +
106C HIS 3.2 0.2 - - - -
107C LEU* 1.3 75.2 - - - +
109C GLN* 1.3 55.9 + - - +
111C VAL* 3.6 7.3 - - - +
112C SER* 2.7 35.5 + - - -
119C ASP* 2.8 45.3 + - + +
120C ASP* 4.7 1.6 - - - +
122C PHE* 3.0 33.2 + - + -
123C TRP* 4.6 4.3 - - + +
124C LEU* 3.8 23.1 - - + +
131C LEU 6.0 0.2 - - - +
133C ASP* 3.7 33.3 + - - +
153C ARG* 4.3 9.5 - - - +
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA* 3.1 25.0 + - - +
106C HIS* 3.5 25.7 - - + +
107C LEU 3.2 0.2 - - - -
108C LYS* 1.3 75.6 - - - +
110C GLN* 1.3 62.8 + - + +
112C SER* 3.6 6.3 - - - -
113C GLY* 3.3 19.4 + - - -
119C ASP* 4.9 11.2 - - - +
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Residues in contact with GLN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 3.5 36.0 - - + +
97C GLU* 3.4 24.1 + - - +
98C VAL* 4.7 2.9 - - - -
102C GLN* 3.4 13.2 + - - -
106C HIS* 3.2 39.8 + - + +
107C LEU* 3.1 10.2 + - - +
109C GLN* 1.3 80.1 - - + +
111C VAL* 1.3 59.5 + - - +
113C GLY* 3.8 0.7 + - - -
114C LEU* 3.3 18.2 + - - +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 4.2 19.5 - - + -
96C TYR* 3.8 29.2 - - + +
107C LEU* 2.9 34.7 + - + +
108C LYS* 3.2 6.3 + - - +
110C GLN* 1.3 75.9 - - - +
112C SER* 1.3 59.8 + - - +
114C LEU* 4.0 0.2 - - - +
115C GLU* 2.8 38.2 + - + +
122C PHE* 3.8 10.5 - - + -
124C LEU* 4.7 4.0 - - + -
150C MET* 3.6 36.8 - - + -
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Residues in contact with SER 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LYS 2.7 21.6 + - - -
109C GLN* 3.6 9.2 - - - -
111C VAL* 1.3 71.6 - - - +
113C GLY* 1.3 56.3 + - - +
115C GLU* 5.1 0.4 - - - -
116C GLY* 2.7 36.9 + - - -
117C VAL 2.8 29.2 + - - +
118C GLN* 4.1 8.8 + - - -
119C ASP* 4.1 12.7 + - - -
122C PHE* 4.3 2.8 - - - -
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLN 3.3 12.3 + - - -
110C GLN 4.2 0.9 - - - -
112C SER* 1.3 79.8 - - - +
114C LEU* 1.3 61.3 + - - +
116C GLY* 3.6 6.8 + - - -
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ARG* 3.8 18.4 + - - +
94C SER* 3.9 19.7 - - - +
95C THR 4.7 4.9 - - - +
96C TYR* 3.2 36.3 - - + +
110C GLN 3.3 17.6 + - - +
112C SER 3.3 0.2 - - - -
113C GLY* 1.3 76.7 - - - +
115C GLU* 1.3 79.5 + - - +
116C GLY* 3.4 0.7 + - - -
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 5.0 3.6 - - - +
88C ASN* 2.6 49.5 + - + +
90C LYS* 4.7 4.9 + - - +
92C ARG* 2.9 21.1 + - - +
94C SER* 5.0 1.6 + - - -
96C TYR* 4.1 5.5 + - - -
111C VAL* 2.8 22.8 + - + +
112C SER 4.4 0.2 - - - +
114C LEU* 1.3 87.7 - - + +
116C GLY* 1.3 63.0 + - - +
117C VAL* 3.5 12.8 + - + +
150C MET* 3.9 25.9 - - + +
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Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER 2.7 18.3 + - - -
113C GLY 4.2 5.4 - - - -
114C LEU 3.2 4.2 - - - -
115C GLU* 1.3 74.4 - - - +
117C VAL* 1.3 59.5 + - - +
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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