Contacts of the helix formed by residues 103 - 113 (chain B) in PDB entry 2YVL
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.3 12.9 - - - -
100B THR* 3.1 15.5 + - - -
101B GLY 3.3 1.0 + - - -
102B SER* 1.3 79.9 - - - +
104B ALA* 1.3 60.0 + - - +
105B LEU 3.5 1.3 - - - -
106B LEU* 3.7 15.5 - - - -
107B ALA 3.0 23.0 + - - -
129B ALA* 4.0 11.4 - - - -
133B LEU* 3.4 7.2 - - - +
602B SAM 3.3 0.4 + - - -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 3.8 22.6 - - + +
68B PHE* 4.0 12.5 - - + -
74B ILE* 3.7 22.7 - - + -
75B ILE 3.4 21.0 - - - +
80B SER* 4.7 0.5 + - - -
102B SER 3.5 1.8 + - - -
103B GLY* 1.3 76.2 - - - +
105B LEU* 1.3 65.3 + - - +
107B ALA* 3.7 8.5 + - - +
108B VAL* 3.7 14.4 - - - +
602B SAM 3.2 10.9 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 3.7 18.1 + - + -
80B SER* 3.7 29.2 - - - +
83B ILE* 4.1 18.8 - - + -
97B GLU* 3.6 18.6 - - + +
104B ALA* 1.3 72.3 - - - +
106B LEU* 1.3 67.3 + - - +
108B VAL* 2.9 16.1 + - + +
109B LEU* 3.0 36.8 + - + +
163B PHE* 3.3 37.7 - - + -
165B ASP* 5.6 0.7 - - + -
602B SAM 3.0 19.4 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 3.4 28.4 + - - +
100B THR* 3.8 14.6 - - + -
103B GLY* 3.4 14.9 + - - +
105B LEU* 1.3 78.0 - - - +
107B ALA* 1.3 54.3 + - - +
109B LEU* 3.2 4.1 + - + +
110B SER* 2.8 36.6 + - - -
116B VAL* 3.6 26.7 - - + -
118B THR* 4.0 3.4 - - + -
133B LEU* 4.0 18.2 - - + -
142B VAL* 3.9 15.5 - - + -
144B PHE* 3.3 39.7 - - + -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.1 10.5 - - + -
64B ILE* 4.4 3.6 - - + -
68B PHE* 3.9 22.2 - - + -
103B GLY 3.0 16.6 + - - +
104B ALA 3.8 7.6 - - - +
105B LEU 3.2 0.4 - - - -
106B LEU* 1.3 75.1 - - - +
108B VAL* 1.3 57.6 + - - +
110B SER* 3.7 2.6 + - - -
111B GLU* 3.2 32.4 + - - +
133B LEU* 3.9 12.1 - - + +
138B LEU* 3.9 16.3 - - + +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.8 11.4 - - + -
60B LEU* 4.3 9.6 - - + -
64B ILE* 3.8 17.3 - - + -
80B SER* 3.4 46.2 - - - +
81B PHE* 3.8 22.2 - - + -
84B ALA* 3.8 12.6 - - + -
104B ALA 3.7 13.7 - - - +
105B LEU* 2.9 6.2 + - + +
107B ALA* 1.3 73.0 - - - +
109B LEU* 1.3 67.9 + - - +
111B GLU* 3.2 2.3 + - - +
112B VAL* 3.0 24.8 + - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 4.8 0.4 - - + -
84B ALA* 4.4 13.7 - - + -
87B LEU* 4.5 12.1 - - + -
89B LEU* 3.8 26.0 - - + -
95B VAL* 4.2 22.0 - - + -
97B GLU* 3.9 33.9 - - + +
105B LEU* 3.0 47.7 + - + +
106B LEU* 3.7 5.6 - - - +
108B VAL* 1.3 75.7 - - - +
110B SER* 1.3 56.1 + - - +
112B VAL 4.6 0.2 - - - +
113B ALA* 2.7 39.4 + - - +
116B VAL* 3.9 8.7 - - + -
163B PHE* 5.0 3.4 - - + -
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LYS* 3.4 6.6 + - - -
106B LEU 2.8 18.3 + - - -
107B ALA* 3.8 7.4 - - - -
109B LEU* 1.3 79.0 - - - +
111B GLU* 1.3 64.0 + - - +
113B ALA 3.6 0.2 - - - +
116B VAL* 3.9 7.1 - - - +
133B LEU* 4.5 1.1 - - - -
138B LEU* 5.1 0.6 - - - +
139B GLY* 3.3 21.7 + - - -
141B ASN* 2.7 47.5 + - - +
142B VAL* 3.7 13.9 - - - -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 5.0 4.7 - - + -
88A ASN* 5.6 1.7 - - - +
89A LEU 4.7 3.6 - - - +
90A ASN* 2.9 49.4 + - + +
112A VAL* 5.7 2.6 - - - +
60B LEU* 4.1 22.5 - - + +
91B LYS* 3.1 18.8 + - - +
107B ALA 3.2 20.0 + - - +
108B VAL* 3.2 7.4 + - - +
110B SER* 1.3 80.6 + - - +
112B VAL* 1.3 63.1 + - + +
138B LEU* 3.6 29.0 - - + +
139B GLY 5.5 0.2 + - - -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.9 28.5 - - + -
111A GLU 6.1 1.1 - - - +
112A VAL* 5.2 9.6 - - + +
84B ALA* 3.9 23.6 - - + +
85B LEU* 4.4 13.7 - - + -
89B LEU* 3.3 36.1 - - + +
90B ASN* 3.2 21.5 - - - -
91B LYS* 3.6 8.3 + - - +
108B VAL 3.0 16.1 + - - +
109B LEU* 4.2 1.3 - - - +
111B GLU* 1.3 78.4 - - - +
113B ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 4.3 15.0 - - + -
90B ASN 3.3 7.0 - - - +
91B LYS* 2.8 22.7 + - - -
93B LYS 3.7 9.2 - - - +
95B VAL* 3.8 25.1 - - + -
109B LEU 2.7 22.2 + - - +
110B SER 3.6 0.5 - - - +
112B VAL* 1.3 74.4 - - - +
114B GLY* 1.3 61.3 + - - +
115B GLU 3.4 5.8 - - - +
116B VAL* 4.4 1.8 - - + -
141B ASN* 2.9 10.5 - - - +
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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