Contacts of the helix formed by residues 97 - 110 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95K ILE 3.7 3.1 - - - +
96K ALA* 1.3 83.3 - - + +
98K GLU* 1.3 78.3 + - - +
99K ILE 3.3 1.2 + - - -
100K ALA* 3.3 17.4 + - + +
101K LEU* 4.6 2.3 + - - +
165L VAL* 5.2 2.0 - - + -
169L LEU* 3.8 39.5 - - + +
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Residues in contact with GLU 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J PRO* 3.9 31.4 - - + +
97J PRO* 4.6 6.5 - - - +
98J GLU* 4.9 23.9 - - + +
96K ALA* 3.6 17.2 - - - +
97K PRO* 1.3 94.4 - - + +
99K ILE* 1.3 60.8 + - + +
100K ALA 3.5 0.2 - - - -
101K LEU* 4.9 3.3 + - - +
102K GLU* 3.7 14.6 + - - +
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Residues in contact with ILE 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J PRO* 4.9 5.4 - - + -
68K HIS* 3.8 39.9 - - + +
69K VAL* 5.1 3.6 - - + -
72K LYS* 4.4 22.7 - - + -
95K ILE* 4.4 5.2 - - + -
96K ALA* 3.2 23.2 + - + +
98K GLU* 1.3 80.5 - - + +
100K ALA* 1.3 55.3 + - - +
101K LEU 3.5 0.7 - - - -
102K GLU* 3.3 8.7 + - - +
103K LEU* 2.8 59.7 + - + +
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Residues in contact with ALA 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ILE* 4.1 10.8 - - + -
96K ALA 3.3 9.7 + - - +
97K PRO* 3.3 16.2 + - + +
99K ILE* 1.3 75.9 - - - +
101K LEU* 1.3 65.9 + - + +
103K LEU* 3.8 2.0 - - - +
104K LEU* 3.0 26.0 + - - +
162L CYS* 4.3 5.3 - - + +
165L VAL* 4.3 19.1 - - + -
166L VAL* 3.8 21.7 - - + +
169L LEU* 4.8 4.0 - - + -
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J GLU* 6.1 1.3 - - - +
97K PRO 4.6 2.3 + - - +
98K GLU 4.9 2.8 + - - +
99K ILE 3.5 0.6 - - - -
100K ALA* 1.3 77.6 - - + +
102K GLU* 1.3 65.4 + - + +
104K LEU* 3.4 9.9 - - + +
105K MET* 3.2 30.7 + - + +
166L VAL* 4.1 21.3 - - + -
178L LEU* 3.8 37.5 - - + -
179L ASP* 5.5 4.3 - - + +
180L ILE* 4.2 22.2 - - + -
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Residues in contact with GLU 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J PRO* 3.4 27.6 - - + +
66K PRO* 4.2 10.5 - - + +
68K HIS* 3.1 33.5 + - - -
69K VAL* 3.5 18.8 - - + +
98K GLU 3.7 12.8 + - - +
99K ILE* 3.3 4.4 + - - +
100K ALA 3.3 0.4 - - - -
101K LEU* 1.3 77.7 - - + +
103K LEU* 1.3 67.0 + - - +
105K MET* 3.3 22.9 + - + +
106K ALA* 2.9 23.0 + - - +
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Residues in contact with LEU 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K VAL* 4.0 11.8 - - + +
72K LYS* 4.2 19.5 - - + -
73K VAL* 3.9 18.8 - - + -
93K PHE* 4.9 1.1 - - + -
95K ILE* 3.8 18.2 - - + -
99K ILE* 2.8 38.3 + - + +
100K ALA* 3.8 1.8 - - - +
102K GLU* 1.3 77.0 - - - +
104K LEU* 1.3 52.9 + - - +
106K ALA* 3.1 1.5 + - + -
107K ALA* 2.6 37.2 + - - +
158L LEU* 3.5 43.5 - - + -
162L CYS* 3.7 12.6 - - - -
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Residues in contact with LEU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K ALA 3.0 17.1 + - - +
101K LEU* 3.4 16.8 - - + +
103K LEU* 1.3 75.1 - - - +
105K MET* 1.3 53.8 - - + +
107K ALA* 3.2 3.1 + - - +
108K ASN* 2.7 31.9 + - - +
159L LYS* 4.6 13.7 - - + -
162L CYS* 3.6 23.9 - - + -
163L LEU* 4.2 26.5 - - + -
166L VAL* 4.3 19.1 - - + -
180L ILE* 4.9 9.9 - - + -
184L LEU* 3.7 36.6 - - + -
188L LEU* 5.3 2.2 - - + -
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Residues in contact with MET 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K LEU* 3.2 21.8 - - + +
102K GLU* 3.3 27.3 + - + +
104K LEU* 1.3 74.4 - - + +
106K ALA* 1.3 67.0 + - - +
108K ASN* 3.6 6.8 - - - +
109K PHE* 3.1 23.6 + - - +
179L ASP 4.6 6.7 - - - +
180L ILE* 4.3 19.1 - - + -
181L VAL* 5.9 3.8 - - + -
184L LEU* 4.1 18.6 - - + -
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Residues in contact with ALA 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K ILE* 4.2 24.9 - - + -
69K VAL* 3.5 30.1 - - + -
73K VAL* 4.5 6.1 - - + -
102K GLU 2.9 8.4 + - - +
103K LEU* 3.4 10.5 - - + +
105K MET* 1.3 75.0 - - - +
107K ALA* 1.3 58.0 + - - +
109K PHE* 3.3 4.6 + - - +
110K LEU* 3.0 36.6 + - + +
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Residues in contact with ALA 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K LEU 2.6 21.0 + - - +
104K LEU* 3.5 5.8 - - - +
106K ALA* 1.3 74.5 - - - +
108K ASN* 1.3 61.1 + - - +
110K LEU* 3.4 0.6 + - - -
111K ASP* 3.1 19.2 + - - -
112K CYS* 3.6 17.1 + - - +
158L LEU* 3.5 36.5 - - + +
159L LYS* 3.7 21.7 - - - +
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Residues in contact with ASN 108 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C ARG* 2.9 37.6 + - - +
104K LEU* 2.7 20.9 + - + +
105K MET* 3.6 7.2 - - - +
107K ALA* 1.3 75.7 - - - +
109K PHE* 1.3 58.9 + - - +
111K ASP 3.7 0.2 + - - -
159L LYS* 3.2 30.0 + - + +
181L VAL* 5.9 3.0 - - - +
183L SER* 4.7 6.3 + - - -
184L LEU* 3.2 35.4 - - + +
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Residues in contact with PHE 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 4.6 7.0 - - + -
106C GLY* 3.0 42.0 - - - -
107C ARG* 3.3 18.6 - - + -
108C ARG* 3.8 12.9 + - - +
41K THR* 2.6 45.8 + - + +
45K MET* 4.5 10.8 - - + -
62K PHE* 4.1 27.8 - + - -
65K ILE* 4.5 11.2 - - + -
105K MET 3.1 16.0 + - - +
106K ALA* 3.7 3.1 - - - +
108K ASN* 1.3 76.0 - - - +
110K LEU* 1.3 63.7 + - + +
111K ASP 3.3 0.6 + - - -
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Residues in contact with LEU 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K SER* 2.3 30.2 + - - +
41K THR* 3.2 13.2 + - + -
42K ILE* 3.9 27.8 - - + -
62K PHE* 4.0 21.5 - - + -
65K ILE* 4.5 11.0 - - + -
70K LEU* 5.5 2.7 - - + -
73K VAL* 3.6 39.9 - - + -
77K PHE* 4.9 2.9 - - + -
106K ALA 3.0 22.6 + - - +
107K ALA 3.4 0.2 + - - -
109K PHE* 1.3 85.9 - - + +
111K ASP* 1.3 71.4 + - - +
112K CYS* 4.0 14.6 - - - -
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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