Contacts of the helix formed by residues 103 - 113 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.2 13.3 - - - -
100A THR* 2.9 16.5 + - - -
101A GLY 3.3 1.2 + - - -
102A SER* 1.3 79.7 - - - +
104A ALA* 1.3 58.2 + - - +
105A LEU 3.5 2.5 - - - -
106A LEU* 3.5 15.3 - - - +
107A ALA 3.0 23.2 + - - -
129A ALA* 3.8 10.7 - - - +
133A LEU* 3.5 6.4 - - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.6 38.0 - - + +
68A PHE* 3.9 12.6 - - + -
74A ILE* 3.6 22.9 - - + -
75A ILE 3.5 20.0 - - - +
80A SER* 4.7 0.3 + - - -
102A SER 3.4 2.2 + - - -
103A GLY* 1.3 75.8 - - - +
105A LEU* 1.3 65.5 + - - +
107A ALA* 3.7 3.5 + - - +
108A VAL* 3.9 4.0 - - - +
601A SAM 3.1 13.3 + - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.7 19.0 + - + -
80A SER* 3.6 35.4 - - - +
83A ILE* 4.1 21.1 - - + -
97A GLU* 3.5 18.8 - - + +
104A ALA* 1.3 70.9 - - - +
106A LEU* 1.3 67.9 - - - +
108A VAL* 2.9 15.8 + - + +
109A LEU* 3.0 30.2 + - + +
163A PHE* 3.3 38.1 - - + -
165A ASP* 5.6 0.2 - - + -
601A SAM 2.8 19.1 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.4 24.4 + - - +
100A THR* 3.7 15.7 - - + -
103A GLY* 3.5 14.3 - - - +
105A LEU* 1.3 78.0 - - - +
107A ALA* 1.3 54.4 + - - +
109A LEU* 3.2 4.2 + - - -
110A SER* 2.7 37.1 + - - -
116A VAL* 3.8 24.5 - - + -
118A THR* 4.1 3.4 - - + -
129A ALA* 5.0 0.2 - - + -
133A LEU* 3.8 19.3 - - + -
142A VAL* 3.8 22.9 - - + -
144A PHE* 3.3 38.1 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.3 3.5 - - + +
64A ILE* 4.1 12.3 - - + -
68A PHE* 3.8 22.2 - - + -
103A GLY 3.0 16.8 + - - +
104A ALA 3.7 8.5 - - - +
105A LEU 3.2 0.4 - - - -
106A LEU* 1.3 74.6 - - - +
108A VAL* 1.3 61.3 - - - +
110A SER* 3.6 3.1 - - - -
111A GLU* 3.2 28.5 + - - +
133A LEU* 4.2 11.9 - - + +
138A LEU* 4.2 15.5 - - + +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.4 3.8 - - + -
64A ILE* 3.8 22.9 - - + -
80A SER* 3.3 47.6 - - - +
81A PHE* 3.8 13.0 - - + -
84A ALA* 3.7 13.2 - - + -
104A ALA 3.9 4.0 - - - +
105A LEU* 2.9 5.9 + - + +
107A ALA* 1.3 74.6 - - - +
109A LEU* 1.3 65.3 + - - +
111A GLU* 3.0 16.4 + - - +
112A VAL* 3.1 13.7 + - - +
85B LEU* 3.9 24.2 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 4.2 14.8 - - + -
87A LEU* 4.4 11.7 - - + -
89A LEU* 3.7 26.0 - - + -
95A VAL* 4.3 14.8 - - + -
97A GLU* 3.8 38.8 - - + -
105A LEU* 3.0 39.9 + - + +
106A LEU* 3.7 6.3 - - - +
108A VAL* 1.3 76.0 - - - +
110A SER* 1.3 57.0 + - - +
112A VAL* 5.0 0.2 - - - -
113A ALA* 2.9 36.4 + - - +
116A VAL* 3.8 14.8 - - + +
163A PHE* 4.8 3.6 - - + -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 3.2 4.3 + - - -
106A LEU 2.7 21.8 + - - -
107A ALA* 3.6 7.9 - - - -
109A LEU* 1.3 74.5 - - - +
111A GLU* 1.3 66.1 + - - +
113A ALA 3.4 0.7 - - - +
116A VAL* 3.9 7.8 - - - +
133A LEU* 4.6 0.9 - - - -
138A LEU* 5.2 0.6 - - - +
139A GLY* 3.3 22.9 + - - -
140A LYS 4.5 0.2 + - - -
141A ASN* 2.7 46.7 + - - +
142A VAL* 3.8 14.1 - - - -
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.1 24.5 - - + +
91A LYS* 2.9 21.3 + - - +
107A ALA 3.2 14.1 + - - +
108A VAL* 3.0 9.6 + - - +
110A SER* 1.3 82.9 + - - +
112A VAL* 1.3 61.9 + - + +
138A LEU* 3.6 29.4 - - + +
85B LEU* 4.9 4.3 - - + -
88B ASN* 5.7 0.9 - - - +
89B LEU 4.6 3.6 - - - +
90B ASN* 3.1 45.9 + - + +
112B VAL* 6.1 1.3 - - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 4.0 20.0 - - + +
85A LEU* 4.1 17.0 - - + -
89A LEU* 3.2 37.5 - - + +
90A ASN* 3.2 18.5 - - - -
91A LYS* 3.6 8.8 + - - +
108A VAL 3.1 15.3 + - - +
109A LEU* 4.3 1.3 - - - +
111A GLU* 1.3 78.6 - - - +
113A ALA* 1.3 63.3 + - - +
85B LEU* 3.9 29.6 - - + -
111B GLU 5.7 2.3 - - - +
112B VAL* 5.2 10.5 - - + +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.2 16.6 - - + -
90A ASN 3.3 6.5 - - - -
91A LYS* 2.8 21.3 + - - -
93A LYS 3.8 8.5 - - - +
95A VAL* 3.7 26.2 - - + -
109A LEU 2.9 21.3 + - - +
112A VAL* 1.3 74.8 - - - +
114A GLY* 1.3 61.1 + - - +
115A GLU 3.5 4.3 - - - +
116A VAL* 4.5 1.6 - - + -
141A ASN* 2.9 12.2 + - - -
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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