Contacts of the helix formed by residues 103 - 115 (chain C) in PDB entry 1T4P
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 MET 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ALA* 4.2 13.9 - - + +
15C PHE* 3.3 43.1 - - + -
55C PHE* 3.8 19.3 - - + -
76C ALA* 3.6 26.0 - - - +
77C ASN* 3.0 24.2 - - - +
80C LEU* 3.3 29.4 - - + +
96C VAL* 5.2 0.4 - - + -
98C GLY* 5.6 0.2 - - - -
99C GLY 5.3 0.4 - - - -
100C ASP 3.4 13.0 - - - +
101C HIS 3.1 0.4 - - - -
102C SER* 1.3 72.9 - - - +
104C ALA* 1.3 55.0 + - - +
105C ILE 3.0 6.6 + - - -
106C GLY 3.2 2.6 + - - -
107C SER* 3.0 24.1 + - - -
276C MET* 3.5 17.3 - - + -
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Residues in contact with ALA 104 (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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101C HIS* 3.3 33.7 + - + +
102C SER 3.0 0.6 - - - -
103C MET* 1.3 76.3 - - - +
105C ILE* 1.3 65.1 + - - +
107C SER* 3.8 10.1 - - - -
108C ILE* 3.0 31.2 + - + +
122C TRP* 3.7 20.2 - - + -
144C PRO* 4.4 2.5 - - + -
148C LEU* 4.1 1.7 - - + +
230C SER* 3.9 8.5 - - - +
274C ASP* 4.7 2.2 - - - +
276C MET* 3.9 4.9 - - + +
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Residues in contact with ILE 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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73C VAL* 5.1 1.1 - - + -
77C ASN* 3.7 8.3 - - + +
102C SER* 3.2 22.0 + - - +
103C MET 3.0 0.8 - - - -
104C ALA* 1.3 78.2 - - - +
106C GLY* 1.3 56.1 + - - +
109C SER* 2.6 40.3 + - - +
140C LEU* 5.4 3.6 - - + +
144C PRO* 3.7 34.3 - - + +
147C PHE* 4.1 20.9 - - + -
148C LEU* 3.8 14.7 - - + +
162C PHE* 3.8 24.7 - - + -
164C TRP* 4.3 5.6 - - + -
165C VAL* 4.1 25.8 - - + -
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Residues in contact with GLY 106 (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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77C ASN* 2.8 43.3 + - - -
80C LEU* 4.3 2.0 - - - -
81C ALA* 3.3 18.5 - - - -
84C VAL* 4.8 0.2 - - - +
103C MET 3.7 0.4 - - - -
105C ILE* 1.3 75.0 - - - +
107C SER* 1.3 58.4 + - - +
110C GLY* 2.8 28.4 + - - -
164C TRP* 4.1 2.2 - - - -
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Residues in contact with SER 107 (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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80C LEU* 3.7 5.5 - - - +
84C VAL* 3.6 19.5 - - - +
94C SER* 5.5 0.9 + - - -
96C VAL* 3.7 16.7 - - - +
103C MET 3.0 17.1 + - - -
104C ALA* 4.0 3.4 - - - -
106C GLY* 1.3 75.9 - - - +
108C ILE* 1.3 61.4 + - - +
111C HIS* 3.2 22.3 + - - +
228C HIS* 3.2 9.8 - - - -
273C LEU 4.8 0.2 + - - -
274C ASP* 2.9 37.6 + - - -
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Residues in contact with ILE 108 (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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104C ALA* 3.0 20.4 + - + +
107C SER* 1.3 73.1 - - - +
109C SER* 1.3 61.4 + - - +
111C HIS* 3.3 2.4 + - - +
112C ALA* 2.8 28.6 + - + +
118C LEU* 4.8 8.1 - - + -
120C VAL* 4.1 26.2 - - + -
122C TRP* 3.8 24.0 - - + -
148C LEU* 3.8 25.6 - - + -
168C CYS* 4.7 5.6 - - - -
169C ILE* 4.6 13.9 - - + -
228C HIS* 3.3 35.9 - - + +
230C SER* 4.7 0.9 - - - -
274C ASP* 4.5 1.1 - - - +
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Residues in contact with SER 109 (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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81C ALA* 4.2 0.9 - - - -
105C ILE* 2.6 27.1 + - - +
106C GLY 3.6 2.9 - - - -
108C ILE* 1.3 78.3 - - - +
110C GLY* 1.3 64.0 + - - +
112C ALA* 3.2 9.5 + - - +
113C ARG* 3.2 21.0 + - - +
148C LEU* 3.6 12.7 - - - +
164C TRP* 4.0 26.1 - - - -
165C VAL* 4.4 6.8 - - - +
166C THR 5.0 2.4 + - - -
168C CYS* 4.1 13.5 - - - -
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Residues in contact with GLY 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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81C ALA* 3.3 29.9 - - - +
84C VAL* 4.1 5.8 - - - -
85C ALA* 3.6 16.7 - - - -
106C GLY 2.8 17.2 + - - -
107C SER 4.1 0.4 - - - -
109C SER* 1.3 72.7 - - - +
111C HIS* 1.3 63.3 + - - +
113C ARG* 3.2 22.0 + - - +
114C VAL* 3.7 1.9 + - - +
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Residues in contact with HIS 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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84C VAL* 3.6 10.7 - - + +
88C GLN* 3.6 21.7 + - - -
94C SER* 5.1 0.4 - - - +
107C SER 3.2 19.1 + - - +
108C ILE 3.5 5.6 - - - +
109C SER 3.2 0.2 - - - -
110C GLY* 1.3 75.0 - - - +
112C ALA* 1.3 58.4 + - - +
114C VAL* 3.1 6.4 + - - +
115C HIS* 2.9 35.3 + - - +
118C LEU* 3.4 20.8 - - + +
226C PRO* 4.4 0.8 - - - +
227C ILE 4.2 2.2 - - - -
228C HIS* 2.9 30.3 + - + +
271C SER* 2.6 35.0 + - - -
272C GLY* 3.4 23.0 - - - -
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Residues in contact with ALA 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 ILE* 2.8 21.3 + - + +
109C SER 3.2 3.8 + - - +
111C HIS* 1.3 73.8 - - - +
113C ARG* 1.3 62.8 + - - +
115C HIS 3.4 11.9 - - - +
116C PRO* 3.0 30.4 - - + +
118C LEU* 3.5 10.3 - - + +
168C CYS* 3.4 34.1 - - + +
169C ILE* 5.3 2.0 - - + -
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Residues in contact with ARG 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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78C GLU* 5.2 3.6 + - - +
81C ALA* 3.7 31.8 + - - +
82C ALA* 3.9 9.5 - - - +
85C ALA* 4.1 18.1 - - + +
109C SER* 3.2 16.6 + - - +
110C GLY* 3.3 7.6 - - - +
111C HIS 3.1 0.6 + - - -
112C ALA* 1.3 77.9 - - - +
114C VAL* 1.3 63.2 + - + +
116C PRO* 4.3 5.2 - - - +
164C TRP* 3.7 35.3 + - - +
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Residues in contact with VAL 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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85C ALA* 3.4 36.1 - - + +
88C GLN* 3.6 31.9 - - + +
89C LYS* 3.7 12.3 - - + +
110C GLY 4.3 0.7 - - - +
111C HIS 3.1 6.3 + - - +
113C ARG* 1.3 81.0 - - + +
115C HIS* 1.3 77.4 + - + +
116C PRO* 3.4 7.4 - - - +
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Residues in contact with HIS 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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88C GLN* 3.5 29.1 + - - -
91C GLY* 6.2 2.0 - - - -
111C HIS* 2.9 25.1 + - + +
112C ALA* 3.2 4.2 - - - -
114C VAL* 1.3 97.6 - - + +
116C PRO* 1.3 64.0 - - - +
117C ASP* 3.2 8.5 + - - +
118C LEU* 3.2 23.7 + - + +
226C PRO* 3.8 31.3 - - + +
271C SER* 4.0 7.0 - - - -
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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