Contacts of the helix formed by residues 99 - 117 (chain C) in PDB entry 6H25
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 GLY 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C LEU* 5.8 2.0 + - - +
93C PHE* 6.2 4.3 - - - -
97C PRO 3.7 2.4 + - - -
98C PRO* 1.3 78.2 - - - +
100C GLU* 1.3 65.8 + - - -
101C GLU* 3.4 2.5 - - - -
102C ALA* 3.7 5.9 + - - +
103C GLN* 3.3 23.7 + - - +
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Residues in contact with GLU 100 (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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99C GLY* 1.3 70.7 - - - -
101C GLU* 1.3 61.6 + - - +
103C GLN* 3.2 10.4 + - - +
104C VAL* 3.0 35.6 + - + +
92D LYS* 4.3 21.9 - - + +
96D ARG* 3.5 24.7 + - - +
99D ARG* 3.1 42.5 + - - -
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.8 20.0 - - + -
93C PHE* 4.1 22.0 - - + -
99C GLY* 3.4 1.0 - - - -
100C GLU* 1.3 78.4 - - - +
102C ALA* 1.3 57.8 + - - +
104C VAL* 3.4 5.9 + - - +
105C ALA* 3.0 29.5 + - - +
144C TYR* 4.6 14.8 + - + +
148C ILE* 4.3 20.1 - - + +
149C LEU* 4.9 6.6 - - - +
96D ARG* 3.4 32.0 + - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL 3.6 17.8 - - - +
85C LEU* 3.6 30.3 - - + +
98C PRO* 4.0 25.6 - - + -
99C GLY* 3.7 6.5 + - - +
100C GLU 3.3 0.6 - - - -
101C GLU* 1.3 78.5 - - - +
103C GLN* 1.3 57.4 + - - +
105C ALA* 3.8 2.7 - - - +
106C SER* 2.8 35.1 + - - -
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PRO* 3.5 20.9 + - + +
99C GLY 3.3 13.1 + - - +
100C GLU* 3.2 7.3 + - - +
102C ALA* 1.3 74.8 - - - +
104C VAL* 1.3 58.5 + - - +
106C SER* 3.3 4.5 + - - -
107C GLN* 3.0 25.3 + - - +
88D GLY 5.4 0.2 - - - +
89D VAL* 3.4 28.8 - - + +
92D LYS* 3.2 39.6 - - + +
6F ARG* 3.3 54.6 - - - +
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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
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100C GLU* 3.0 23.7 + - + +
101C GLU* 3.8 4.5 - - - +
103C GLN* 1.3 77.1 - - + +
105C ALA* 1.3 56.0 + - - +
107C GLN* 3.3 4.0 + - - +
108C PHE* 2.9 28.8 + - + +
149C LEU* 6.3 4.3 - - + -
236C HIS* 4.7 19.5 - - + +
92D LYS* 4.8 1.1 - - + +
93D SER* 4.1 31.2 - - - +
96D ARG* 3.6 45.1 - - + +
97D LEU* 6.1 1.3 - - + -
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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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83C VAL* 4.1 21.8 - - + -
85C LEU* 5.6 2.0 - - + -
101C GLU* 3.0 19.0 + - - +
102C ALA* 3.9 3.8 - - - +
104C VAL* 1.3 77.5 - - - +
106C SER* 1.3 57.5 + - - +
108C PHE* 3.2 8.2 + - - +
109C ILE* 2.9 35.0 + - + +
148C ILE* 4.9 17.7 - - + -
149C LEU* 5.2 10.5 - - + -
152C CYS* 5.3 3.4 - - - -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 4.5 4.5 - - - +
82C ASN* 3.7 11.4 + - - +
83C VAL* 3.0 35.2 + - - +
102C ALA 2.8 23.0 + - - -
103C GLN* 3.7 7.2 - - - -
105C ALA* 1.3 76.8 - - - +
107C GLN* 1.3 56.2 + - - +
109C ILE* 3.4 3.7 + - - +
110C ALA* 2.9 29.0 + - - +
89D VAL* 5.0 1.6 - - - -
7F ARG* 6.3 1.3 - - - -
8F ILE* 4.6 18.0 - - - +
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Residues in contact with GLN 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN 3.0 17.6 + - - +
104C VAL 3.9 3.0 - - - +
106C SER* 1.3 76.5 - - - +
108C PHE* 1.3 57.7 + - - +
110C ALA* 3.6 7.4 - - + +
111C ASP* 3.0 56.3 + - - +
236C HIS* 6.1 0.7 - - - -
89D VAL* 4.2 10.2 - - + +
90D ALA* 4.0 30.0 - - + +
93D SER* 3.5 24.7 + - - +
198D LYS* 5.4 9.3 - - - +
8F ILE* 5.0 6.3 - - + -
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Residues in contact with PHE 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 VAL* 2.9 15.9 + - + +
105C ALA* 3.4 12.1 - - - +
107C GLN* 1.3 77.1 + - - +
109C ILE* 1.3 78.5 + - + +
111C ASP* 2.8 22.8 - - - +
112C VAL* 3.0 27.6 + - + +
149C LEU* 3.6 50.7 - - + -
153C THR* 5.2 3.1 - - - -
195C ALA* 4.8 3.8 - - + -
223C THR* 3.7 7.2 - - + -
225C VAL* 3.7 25.8 - - + -
234C CYS* 3.6 20.0 - - - -
236C HIS* 4.0 28.3 - + + -
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Residues in contact with ILE 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 PRO* 3.7 24.0 - - + -
83C VAL* 3.8 21.8 - - + -
105C ALA* 2.9 17.4 + - + +
106C SER* 3.9 3.4 - - - +
108C PHE* 1.3 88.6 - - + +
110C ALA* 1.3 61.4 + - - +
112C VAL* 3.4 5.3 + - + +
113C ILE* 3.0 24.8 + - + +
139C LEU* 5.0 3.6 - - + -
149C LEU* 4.7 0.4 - - - +
152C CYS* 3.8 26.7 - - + -
153C THR* 4.0 18.8 - - - +
156C LEU* 3.7 26.2 - - + -
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.8 21.0 - - + +
106C SER 2.9 17.5 + - - +
107C GLN* 3.6 12.1 - - + +
108C PHE 3.2 0.2 - - - -
109C ILE* 1.3 77.1 - - - +
111C ASP* 1.3 59.5 + - + +
113C ILE* 3.3 5.5 + - - +
114C GLU* 2.9 26.2 + - - +
8F ILE* 5.0 15.0 - - + -
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Residues in contact with ASP 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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107C GLN* 3.0 41.7 + - - +
108C PHE* 2.8 34.3 - - - +
110C ALA* 1.3 73.6 - - - +
112C VAL* 1.3 64.6 + - - +
114C GLU* 3.7 8.3 - - + -
115C ASN* 2.9 47.4 + - - +
234C CYS* 4.9 8.6 - - - +
197D THR 4.4 10.9 - - - +
198D LYS* 5.6 9.1 + - + +
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Residues in contact with VAL 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 PHE* 3.0 39.8 + - + +
109C ILE* 3.7 7.2 - - + +
111C ASP* 1.3 76.8 + - - +
113C ILE* 1.3 57.6 + - + +
115C ASN* 5.0 1.3 - - - -
116C SER* 2.8 45.5 + - - +
118C ILE* 5.9 0.4 - - + -
153C THR* 4.3 18.4 - - - +
156C LEU* 5.6 4.5 - - + -
193C PRO* 4.6 8.5 - - + -
225C VAL* 4.2 19.3 - - + -
233C CYS* 5.4 3.8 - - + -
234C CYS* 3.8 27.6 - - - -
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Residues in contact with ILE 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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79C VAL* 4.0 36.1 - - + -
81C PRO* 4.0 26.9 - - + -
109C ILE* 3.0 18.7 + - + +
110C ALA* 3.6 4.7 - - - +
112C VAL* 1.3 77.6 - - + +
114C GLU* 1.3 62.3 + - - +
116C SER* 3.9 4.2 + - - -
117C GLN* 3.5 17.5 + - - -
118C ILE* 4.4 14.8 + - + -
119C ILE* 4.9 12.0 - - + +
121C LYS* 4.6 8.8 + - - +
137C CYS* 5.5 0.9 - - - -
156C LEU* 3.7 34.5 - - + -
160C LEU* 6.2 1.8 - - + -
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Residues in contact with GLU 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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76C LYS* 6.0 0.2 + - - -
110C ALA 2.9 16.6 + - - +
111C ASP* 3.9 10.1 - - + +
112C VAL 3.2 0.2 - - - -
113C ILE* 1.3 80.1 - - - +
115C ASN* 1.3 67.3 + - - +
117C GLN* 3.9 15.9 + - - +
121C LYS* 4.0 23.2 + - - +
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Residues in contact with ASN 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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111C ASP* 2.9 34.6 + - - +
112C VAL* 4.4 1.3 - - - +
114C GLU* 1.3 83.7 - - - +
116C SER* 1.3 64.8 + - - +
117C GLN* 3.5 2.6 + - - +
233C CYS* 4.0 15.3 + - + +
234C CYS* 4.8 4.2 - - + +
197D THR 3.8 20.4 + - - -
198D LYS* 3.6 12.6 - - - +
199D GLY* 3.3 34.4 + - - +
200D LEU* 3.3 23.2 - - - +
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Residues in contact with SER 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 VAL 2.8 22.4 + - - -
113C ILE 3.9 0.5 + - - -
115C ASN* 1.3 78.1 - - - +
117C GLN* 1.3 69.6 + - - +
118C ILE* 2.7 33.7 + - - +
191C THR* 3.9 16.6 + - - +
193C PRO* 4.0 8.9 - - - +
227C ASP* 6.6 0.2 - - - -
233C CYS* 3.7 29.3 - - - -
200D LEU* 4.0 12.6 - - - +
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Residues in contact with GLN 117 (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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113C ILE 3.5 9.6 + - - -
114C GLU 3.9 13.5 + - - +
115C ASN 3.3 3.9 - - - +
116C SER* 1.3 83.0 + - - +
118C ILE* 1.3 64.9 + - - +
119C ILE* 3.2 14.4 + - - +
120C GLN* 5.1 8.2 + - + +
121C LYS* 5.5 6.1 - - - +
190C ARG* 3.8 15.8 - - - +
191C THR* 4.0 2.8 + - - +
200D LEU* 5.5 5.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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