Contacts of the helix formed by residues 89 - 102 (chain A) in PDB entry 2YVX
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 SER 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLU* 5.5 8.4 + - - -
87A GLU 4.1 1.8 + - - -
88A LEU* 1.3 77.3 - - - +
90A LEU* 1.3 59.0 + - - +
91A ASP* 3.2 19.6 + - - -
92A ASP* 3.5 17.6 + - - +
93A LEU* 3.0 22.7 + - - +
141A GLU* 3.6 13.5 + - - -
166A GLU* 3.7 17.3 + - - +
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Residues in contact with LEU 90 (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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88A LEU 3.3 2.5 + - - -
89A SER* 1.3 67.7 - - - +
91A ASP* 1.3 56.4 + - - +
93A LEU* 3.0 10.5 + - + +
94A ALA* 2.8 33.6 + - + -
119A THR* 4.8 12.6 - - + -
122A GLU* 4.0 21.8 - - + -
123A VAL* 4.7 13.7 - - + -
126A LEU* 3.1 37.2 - - + -
140A PRO* 3.2 31.4 - - + -
141A GLU* 3.1 29.0 + - + +
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Residues in contact with ASP 91 (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 SER* 3.2 8.1 + - - -
90A LEU* 1.3 83.9 - - - +
92A ASP* 1.3 76.8 + - - +
93A LEU 3.1 0.9 + - - -
94A ALA* 3.2 6.2 + - - +
95A ASP* 3.2 26.6 + - - +
126A LEU* 4.8 0.4 - - - -
136A GLY 6.3 0.2 - - - -
137A LEU* 3.8 13.3 - - - +
138A MET 4.1 4.5 - - - +
139A THR* 3.2 33.7 - - + +
166A GLU* 3.2 9.5 - - - +
247A ASP* 2.8 16.5 - - - +
452A MG 2.0 32.5 - - - -
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Residues in contact with ASP 92 (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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59A GLU* 5.1 4.3 - - - +
62A SER* 3.2 35.7 + - - +
63A HIS* 4.3 9.7 + - - -
88A LEU* 4.8 5.6 - - + -
89A SER* 3.6 21.0 - - - +
90A LEU 3.2 0.2 - - - -
91A ASP* 1.3 96.9 + - - +
93A LEU* 1.3 57.6 + - - +
95A ASP* 4.3 3.2 - - - +
96A ALA* 2.9 30.9 + - - +
166A GLU* 5.6 0.2 - - - +
247A ASP* 4.3 3.8 - - - +
452A MG 3.3 11.6 - - - -
226B ASP* 5.7 0.3 - - - +
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Residues in contact with LEU 93 (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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85A LEU* 3.3 42.8 - - + +
88A LEU* 3.6 19.9 - - + +
89A SER 3.0 13.4 + - - +
90A LEU* 3.0 15.5 + - - +
92A ASP* 1.3 74.5 - - - +
94A ALA* 1.3 60.9 + - - +
96A ALA* 2.7 4.1 + - + -
97A LEU* 2.5 54.0 + - + +
115A LEU* 4.0 12.1 - - + -
119A THR* 4.6 7.6 - - + -
123A VAL* 3.3 37.7 - - + -
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Residues in contact with ALA 94 (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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90A LEU* 2.8 15.2 + - + +
91A ASP* 3.5 9.0 - - - +
93A LEU* 1.3 77.0 - - - +
95A ASP* 1.3 63.4 + - - +
97A LEU* 3.3 2.5 + - - +
98A GLN* 2.9 30.1 + - - +
123A VAL* 4.2 18.6 - - + +
126A LEU* 3.9 38.8 - - + +
136A GLY* 6.5 0.2 - - - -
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Residues in contact with ASP 95 (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 ASP* 3.2 13.3 + - - +
92A ASP* 4.3 4.3 - - - +
93A LEU 3.2 0.4 - - - -
94A ALA* 1.3 80.9 - - - +
96A ALA* 1.3 61.8 + - - +
98A GLN* 2.9 24.4 + - - +
99A ALA* 3.2 16.8 + - - +
126A LEU 5.7 0.3 - - - +
131A GLU* 5.9 5.6 - - - +
136A GLY* 2.6 36.5 - - - +
137A LEU* 4.5 6.6 - - - +
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Residues in contact with ALA 96 (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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61A LEU* 6.2 1.1 - - + -
62A SER* 5.4 2.7 - - - -
69A GLN* 2.7 37.0 - - - +
73A LEU* 4.7 8.0 - - + +
88A LEU* 5.2 6.3 - - + -
92A ASP 2.9 22.8 + - - +
93A LEU* 2.7 10.4 + - - +
95A ASP* 1.3 70.5 - - - +
97A LEU* 1.3 65.4 + - - +
99A ALA* 2.9 23.1 + - - +
100A VAL* 3.7 5.2 + - - +
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Residues in contact with LEU 97 (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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73A LEU* 5.4 3.4 - - - -
85A LEU* 5.4 2.5 - - + -
93A LEU* 2.5 43.0 + - + +
94A ALA 3.5 4.3 - - - +
96A ALA* 1.3 73.4 - - - +
98A GLN* 1.3 61.8 + - + +
100A VAL* 3.3 23.8 + - + +
101A ARG 3.8 1.7 + - - -
108A PHE* 3.1 43.3 - - + +
111A LEU* 5.0 18.2 - - + -
112A LYS* 5.1 14.6 - - + -
115A LEU* 4.0 15.3 - - + -
123A VAL* 3.7 27.6 - - + -
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Residues in contact with GLN 98 (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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94A ALA* 2.9 21.3 - - - +
95A ASP* 2.9 34.9 + - - +
96A ALA 3.1 0.6 - - - -
97A LEU* 1.3 73.8 - - + +
99A ALA* 1.3 65.8 + - - +
100A VAL 2.9 2.2 - - - -
101A ARG* 2.8 26.4 + - + +
102A LYS* 3.4 11.8 + - + +
108A PHE* 4.7 7.0 - - + -
126A LEU 3.8 6.9 + - - -
127A ALA* 3.7 36.5 + - + +
129A TYR 4.8 4.9 + - - -
131A GLU* 4.8 24.4 + - - +
136A GLY* 5.8 2.3 - - - -
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Residues in contact with ALA 99 (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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66A PRO* 2.9 45.0 - - + +
67A GLU* 5.9 0.7 - - - +
69A GLN* 4.6 1.3 - - + -
70A ALA* 3.8 7.1 - - + +
95A ASP 3.2 5.9 + - - +
96A ALA* 2.9 20.7 + - - +
98A GLN* 1.3 77.5 - - - +
100A VAL* 1.3 62.3 + - - +
102A LYS* 3.5 21.1 + - - +
103A GLU* 3.7 12.0 - - - +
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Residues in contact with VAL 100 (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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70A ALA* 3.3 26.9 - - + +
73A LEU* 3.5 29.2 - - + -
74A LYS* 5.7 2.7 - - + -
96A ALA 4.4 1.6 - - - +
97A LEU* 3.4 15.3 - - + +
98A GLN 2.9 0.4 - - - -
99A ALA* 1.3 76.8 - - - +
101A ARG* 1.3 53.4 + - - +
103A GLU* 2.7 29.1 + - + +
104A ASP* 2.9 18.7 + - + +
107A TYR* 3.6 37.9 - - + -
108A PHE* 4.4 8.3 - - + +
111A LEU* 5.9 4.7 - - + -
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Residues in contact with ARG 101 (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 LEU 3.8 1.0 + - - -
98A GLN* 2.8 19.3 + - + +
100A VAL* 1.3 74.3 - - - +
102A LYS* 1.3 56.9 + - + +
103A GLU 2.9 5.2 + - - -
104A ASP 3.8 14.3 + - - -
105A PRO* 3.8 35.3 + - - +
108A PHE* 3.8 44.7 - - + -
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Residues in contact with LYS 102 (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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66A PRO* 5.8 9.4 - - + +
67A GLU* 6.5 1.1 - - + -
98A GLN* 3.4 11.3 + - + +
99A ALA* 3.8 14.6 - - - +
100A VAL 3.0 1.4 + - - -
101A ARG* 1.3 76.8 - - + +
103A GLU* 1.3 63.1 + - + +
131A GLU* 4.1 26.5 + - - -
270A ASP* 5.9 4.4 - - - +
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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