Contacts of the helix formed by residues 103 - 113 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C PHE* 3.4 12.4 - - - -
100C THR* 3.0 16.1 + - - -
101C GLY 3.4 0.4 - - - -
102C SER* 1.3 78.8 - - - +
104C ALA* 1.3 59.6 + - - +
105C LEU 3.5 1.8 - - - -
106C LEU* 3.4 16.7 - - - +
107C ALA 3.0 23.4 + - - -
129C ALA* 3.9 12.3 - - - +
133C LEU* 3.5 6.8 - - - +
604C SAM 3.3 0.2 + - - -
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Residues in contact with ALA 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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64C ILE* 3.7 37.4 - - + +
68C PHE* 4.1 13.5 - - + -
74C ILE* 3.7 20.4 - - + -
75C ILE 3.6 17.8 - - - +
80C SER* 4.7 0.7 + - - -
102C SER 3.4 1.8 - - - -
103C GLY* 1.3 75.3 - - - +
105C LEU* 1.3 65.0 + - - +
107C ALA* 3.8 4.3 + - - +
108C VAL* 3.8 4.0 - - - +
604C SAM 3.2 17.3 + - - +
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Residues in contact with LEU 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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75C ILE* 3.8 16.7 + - + -
80C SER* 3.7 28.9 - - - +
83C ILE* 4.0 17.9 - - + -
97C GLU* 3.5 19.7 - - + +
104C ALA* 1.3 72.3 - - - +
106C LEU* 1.3 65.9 + - - +
108C VAL* 2.9 14.7 + - + +
109C LEU* 3.0 37.1 + - + -
163C PHE* 3.3 40.6 - - + -
165C ASP* 5.8 0.2 - - + -
604C SAM 3.0 17.9 + - - +
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Residues in contact with LEU 106 (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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97C GLU* 3.4 23.8 + - - +
100C THR* 3.7 15.5 - - + -
103C GLY* 3.4 15.0 - - - +
104C ALA 3.4 0.4 - - - -
105C LEU* 1.3 78.2 - - - +
107C ALA* 1.3 52.6 + - - +
109C LEU* 3.3 4.7 + - + -
110C SER* 2.8 36.7 + - - -
116C VAL* 3.5 32.3 - - + -
118C THR* 3.9 4.0 - - + -
133C LEU* 3.9 17.9 - - + -
142C VAL* 3.9 15.5 - - + -
144C PHE* 3.4 38.8 - - + -
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Residues in contact with ALA 107 (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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60C LEU* 4.3 11.6 - - + +
64C ILE* 4.3 2.9 - - + -
68C PHE* 3.9 22.7 - - + -
103C GLY 3.0 17.1 + - - +
104C ALA 3.8 7.4 - - - +
105C LEU 3.1 0.4 + - - -
106C LEU* 1.3 75.5 - - - +
108C VAL* 1.3 60.4 + - - +
110C SER* 3.8 2.3 - - - -
111C GLU* 3.3 29.1 + - - +
133C LEU* 4.1 11.9 - - + -
138C LEU* 4.1 15.5 - - + +
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Residues in contact with VAL 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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60C LEU* 4.3 8.3 - - + -
64C ILE* 3.7 24.7 - - + -
80C SER* 3.4 43.1 - - - +
81C PHE* 3.7 22.2 - - + -
84C ALA* 3.7 13.5 - - + -
104C ALA 3.8 5.8 - - - +
105C LEU* 2.9 6.8 + - + +
107C ALA* 1.3 75.7 - - - +
109C LEU* 1.3 64.3 + - - +
111C GLU* 3.2 3.2 + - - +
112C VAL* 3.1 23.4 + - - +
85D LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 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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83C ILE* 4.8 0.2 - - + -
84C ALA* 4.4 14.1 - - + -
87C LEU* 4.6 11.0 - - + -
89C LEU* 3.8 25.8 - - + -
95C VAL* 4.3 16.2 - - + -
97C GLU* 3.8 34.3 - - + -
105C LEU* 3.0 43.7 + - + +
106C LEU* 3.6 7.6 - - - +
108C VAL* 1.3 75.6 - - - +
110C SER* 1.3 54.5 + - - +
112C VAL 4.7 0.2 - - - +
113C ALA* 2.8 40.0 + - - +
116C VAL* 3.9 14.1 - - + -
163C PHE* 5.0 3.6 - - + -
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Residues in contact with SER 110 (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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91C LYS* 3.3 4.9 + - - -
106C LEU 2.8 19.3 + - - -
107C ALA* 3.8 7.4 - - - -
109C LEU* 1.3 77.6 - - - +
111C GLU* 1.3 64.0 + - - +
113C ALA 3.3 0.5 - - - +
116C VAL* 3.9 7.1 - - - +
133C LEU* 4.6 0.4 - - - -
138C LEU* 5.7 0.7 - - - -
139C GLY* 3.2 24.1 + - - -
141C ASN* 2.6 48.8 + - - -
142C VAL* 3.7 13.7 - - - -
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Residues in contact with GLU 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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60C LEU* 4.2 20.5 - - + +
91C LYS* 3.1 20.2 + - - +
107C ALA 3.3 16.4 + - - +
108C VAL 3.2 7.0 + - - +
110C SER* 1.3 81.3 + - - +
112C VAL* 1.3 62.7 + - + +
137C ASN 5.5 0.3 - - - +
138C LEU* 3.7 30.2 - - + +
85D LEU* 5.6 2.2 - - + -
89D LEU 4.7 4.8 - - - +
90D ASN* 3.0 46.8 + - + +
91D LYS 5.6 0.2 + - - -
112D VAL* 5.7 1.9 - - - +
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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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84C ALA* 4.0 20.2 - - + +
85C LEU* 4.1 17.3 - - + -
89C LEU* 3.4 35.0 - - + +
90C ASN* 3.2 22.5 - - - -
91C LYS* 3.6 7.4 + - - +
108C VAL 3.1 16.8 + - - +
109C LEU 4.2 1.6 - - - +
111C GLU* 1.3 81.9 - - + +
113C ALA* 1.3 60.1 + - - +
85D LEU* 4.0 30.5 - - + -
111D GLU 5.7 2.3 - - - +
112D VAL* 5.2 7.2 - - + -
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 4.3 15.7 - - + -
90C ASN 3.3 6.7 - - - +
91C LYS* 2.8 21.5 + - - -
93C LYS 3.8 8.3 - - - +
95C VAL* 3.7 25.8 - - + -
109C LEU 2.8 21.8 + - - +
110C SER 3.3 0.2 - - - +
112C VAL* 1.3 74.0 - - - +
114C GLY* 1.3 61.3 + - - +
115C GLU 3.4 4.5 - - - +
116C VAL* 4.5 1.8 - - + -
141C ASN* 2.9 11.7 + - - -
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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