Contacts of the helix formed by residues 97 - 110 (chain H) in PDB entry 1VCB
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 PRO 97 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H ILE 3.6 3.8 - - - +
96H ALA* 1.3 83.3 - - + +
98H GLU* 1.3 79.7 + - - +
99H ILE 3.3 1.0 + - - -
100H ALA* 3.3 18.3 + - + +
101H LEU* 4.6 2.1 + - - +
165I VAL* 5.0 2.2 - - + -
169I LEU* 3.7 40.4 - - + +
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Residues in contact with GLU 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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96G PRO* 3.7 31.3 - - + +
97G PRO* 4.4 7.5 - - - +
98G GLU* 4.7 26.2 - - + +
96H ALA* 3.3 17.2 + - - +
97H PRO* 1.3 93.4 - - + +
99H ILE* 1.3 60.5 + - + +
100H ALA 3.4 0.2 - - - -
101H LEU* 4.9 3.5 + - - +
102H GLU* 3.7 14.4 + - - +
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Residues in contact with ILE 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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96G PRO* 4.6 7.0 - - + -
68H HIS* 3.8 42.4 - - + +
69H VAL* 5.1 3.6 - - + -
72H LYS* 4.4 20.4 - - + -
95H ILE* 4.4 4.7 - - + -
96H ALA* 3.2 23.6 + - + +
98H GLU* 1.3 80.5 - - + +
100H ALA* 1.3 55.3 + - - +
101H LEU 3.5 0.9 - - - -
102H GLU* 3.3 8.7 + - - +
103H LEU* 2.8 59.4 + - + +
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Residues in contact with ALA 100 (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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95H ILE* 4.1 11.0 - - + -
96H ALA 3.3 9.5 + - - +
97H PRO* 3.3 16.0 + - + +
99H ILE* 1.3 77.4 - - - +
101H LEU* 1.3 64.1 + - + +
103H LEU* 3.8 1.5 - - - +
104H LEU* 3.0 26.0 + - - +
162I CYS* 4.2 5.0 - - - +
165I VAL* 4.1 20.2 - - + -
166I VAL* 3.8 20.9 - - + -
169I LEU* 4.7 4.0 - - + -
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Residues in contact with LEU 101 (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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98G GLU* 5.7 4.7 - - - +
97H PRO 4.6 2.3 + - - +
98H GLU 4.9 2.8 + - - +
99H ILE 3.5 0.6 - - - -
100H ALA* 1.3 76.8 - - + +
102H GLU* 1.3 64.8 + - + +
104H LEU* 3.4 9.1 - - + +
105H MET* 3.2 30.8 + - + +
166I VAL* 3.9 22.4 - - + -
178I LEU* 3.8 39.5 - - + -
179I ASP 5.6 3.6 - - - +
180I ILE* 4.3 18.6 - - + -
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Residues in contact with GLU 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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97G PRO* 3.1 30.0 - - + +
66H PRO* 4.2 10.9 - - + +
68H HIS* 3.1 34.1 + - - -
69H VAL* 3.5 18.1 - - + +
98H GLU 3.7 11.7 + - - +
99H ILE* 3.3 3.7 + - - +
100H ALA 3.3 0.4 - - - -
101H LEU* 1.3 78.1 - - + +
103H LEU* 1.3 67.6 + - - +
105H MET* 3.3 22.0 + - + +
106H ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H VAL* 4.0 12.1 - - + +
72H LYS* 4.1 20.6 - - + -
73H VAL* 3.9 19.1 - - + -
93H PHE* 4.8 1.3 - - + -
95H ILE* 3.8 17.9 - - + -
99H ILE* 2.8 41.4 + - + +
100H ALA* 3.8 2.0 - - - +
102H GLU* 1.3 73.9 - - - +
104H LEU* 1.3 52.9 + - - +
106H ALA 3.1 0.5 + - - -
107H ALA* 2.6 34.8 + - - +
158I LEU* 3.5 42.8 - - + -
162I CYS* 3.7 11.4 - - - -
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Residues in contact with LEU 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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100H ALA 3.0 16.5 + - - +
101H LEU* 3.4 17.0 - - + +
103H LEU* 1.3 76.0 - - - +
105H MET* 1.3 52.0 - - - +
107H ALA* 3.3 2.5 + - - +
108H ASN* 2.7 31.5 + - - +
159I LYS* 4.6 10.8 - - + -
162I CYS* 3.5 25.0 - - + -
163I LEU* 4.2 30.3 - - + +
166I VAL* 4.3 18.6 - - + -
180I ILE* 5.0 10.1 - - + -
184I LEU* 3.9 35.2 - - + -
188I LEU* 5.3 2.5 - - + -
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Residues in contact with MET 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 LEU* 3.2 21.1 - - + +
102H GLU* 3.3 27.3 + - + +
104H LEU* 1.3 73.6 - - + +
106H ALA* 1.3 66.8 + - - +
108H ASN* 3.6 6.5 - - - +
109H PHE* 3.1 23.4 + - - +
179I ASP 4.6 7.6 - - - +
180I ILE* 4.2 21.1 - - + -
181I VAL* 5.8 3.1 - - + -
184I LEU* 4.1 19.1 - - + -
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Residues in contact with ALA 106 (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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65H ILE* 4.1 24.7 - - + -
69H VAL* 3.5 30.7 - - + -
73H VAL* 4.5 6.5 - - + -
102H GLU 2.9 8.1 + - - +
103H LEU* 3.4 10.5 - - + +
105H MET* 1.3 75.6 - - - +
107H ALA* 1.3 58.6 + - - +
109H PHE* 3.2 4.2 + - - +
110H LEU* 2.9 36.7 + - - +
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Residues in contact with ALA 107 (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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103H LEU 2.6 21.4 + - - +
104H LEU* 3.6 5.2 - - - +
106H ALA* 1.3 75.5 - - - +
108H ASN* 1.3 62.3 + - - +
110H LEU* 3.4 0.6 + - - -
111H ASP* 3.1 19.2 + - - -
112H CYS* 3.6 16.6 + - - +
158I LEU* 3.4 37.2 - - + +
159I LYS* 3.7 21.5 - - - +
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Residues in contact with ASN 108 (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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108F ARG* 3.3 28.1 + - - +
104H LEU* 2.7 18.6 + - + +
105H MET* 3.6 7.6 - - - +
107H ALA* 1.3 79.2 - - - +
109H PHE* 1.3 60.9 + - - +
111H ASP* 3.7 0.6 + - - +
159I LYS* 3.1 30.9 + - + +
181I VAL* 5.9 2.2 - - - +
183I SER* 4.8 6.1 + - - -
184I LEU* 3.2 35.5 - - + +
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Residues in contact with PHE 109 (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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75F ILE* 5.0 4.7 - - + -
106F GLY* 2.9 43.3 - - - -
107F ARG* 3.4 17.3 - - + -
108F ARG* 4.1 12.5 + - + +
41H THR* 2.6 46.4 + - + -
45H MET* 4.5 10.5 - - + -
62H PHE* 4.1 25.1 - + - -
65H ILE* 4.5 10.8 - - + -
105H MET 3.1 16.0 + - - +
106H ALA* 3.7 3.6 - - - +
108H ASN* 1.3 80.1 - - - +
110H LEU* 1.3 62.2 + - + +
111H ASP 3.5 0.3 + - - -
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Residues in contact with LEU 110 (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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39H SER* 2.4 29.9 + - - +
41H THR* 3.2 12.3 + - + -
42H ILE* 4.0 27.8 - - + -
62H PHE* 4.0 21.5 - - + -
65H ILE* 4.5 11.2 - - + -
70H LEU* 5.4 2.7 - - + -
73H VAL* 3.6 40.4 - - + -
77H PHE* 4.9 2.5 - - + -
106H ALA 2.9 23.1 + - - +
109H PHE* 1.3 85.5 - - + +
111H ASP* 1.3 71.5 + - - +
112H CYS* 4.0 14.8 - - - -
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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