Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 1YFJ
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 ASP 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ARG* 2.7 34.7 + - - -
94A TYR* 3.2 15.2 - - - -
97A THR* 3.2 19.3 + - - +
98A ARG* 1.3 75.4 - - - +
100A PRO* 1.3 68.5 - - - +
101A LEU* 3.0 15.5 + - - +
102A LEU* 3.0 29.0 + - + +
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Residues in contact with PRO 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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54A PRO 5.2 1.3 - - - +
57A GLU* 3.9 24.9 - - + +
58A MET* 3.5 29.2 - - + +
61A ARG* 3.8 17.7 - - + +
62A LEU* 6.3 0.2 - - - -
94A TYR* 4.4 3.4 - - + +
98A ARG 3.1 10.3 - - - +
99A ASP* 1.3 89.8 - - - +
101A LEU* 1.3 61.2 + - - +
103A LEU* 3.1 11.6 + - + +
104A TYR* 2.9 22.7 + - - +
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Residues in contact with LEU 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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61A ARG* 3.9 30.0 - - + +
62A LEU* 4.5 5.2 - - + -
65A VAL* 4.4 15.7 - - + -
69A ASP* 4.3 18.8 - - + +
70A VAL* 4.4 14.6 - - + -
73A VAL* 3.9 26.7 - - + -
99A ASP* 3.0 18.1 + - - +
100A PRO* 1.3 78.1 - - - +
102A LEU* 1.3 58.8 + - + +
104A TYR* 3.2 20.6 + - + +
105A VAL* 2.9 28.0 + - + +
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Residues in contact with LEU 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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73A VAL* 3.8 22.4 - - + -
77A TYR* 4.4 9.2 - - + +
90A LEU* 3.7 22.7 - - + +
93A ASP* 4.3 9.2 - - + -
94A TYR* 3.9 26.5 - - + +
97A THR* 3.6 25.1 - - + +
99A ASP* 3.0 25.0 + - + +
101A LEU* 1.3 75.8 - - + +
103A LEU* 1.3 60.5 + - - +
105A VAL* 3.0 5.8 + - - +
106A LEU* 2.7 33.6 + - - +
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Residues in contact with LEU 103 (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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54A PRO* 3.4 37.7 - - + +
55A ILE* 4.3 5.6 - - + +
58A MET* 4.0 16.6 - - + -
94A TYR* 3.4 40.4 - - + +
99A ASP 3.4 2.6 + - - -
100A PRO* 3.1 9.3 + - + +
102A LEU* 1.3 77.9 - - - +
104A TYR* 1.3 63.4 + - - +
106A LEU* 3.2 2.2 + - - -
107A HIS* 3.1 21.3 + - - +
115A ILE* 4.3 12.8 - - + -
117A ILE* 4.3 4.0 - - + -
123A PHE* 3.6 34.3 - - + -
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Residues in contact with TYR 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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4A ALA 4.6 4.2 + - - -
5A ILE* 3.9 21.1 - - + -
58A MET* 3.5 29.2 - - + -
62A LEU* 3.6 37.8 - - + +
67A TRP* 3.8 2.1 - + - -
70A VAL* 3.7 30.3 - - + -
100A PRO 2.9 12.9 + - - +
101A LEU* 3.3 13.9 - - + +
102A LEU 3.1 0.4 - - - -
103A LEU* 1.3 78.0 - - - +
105A VAL* 1.3 61.4 + - - +
107A HIS* 2.8 29.8 + + - -
108A PHE* 3.4 36.6 - + - -
136A SER 4.4 1.0 + - - -
140A PHE* 3.3 30.7 + + - +
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Residues in contact with VAL 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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70A VAL* 4.2 19.5 - - + +
73A VAL* 4.0 31.4 - - + -
74A ILE* 3.9 16.6 - - + -
79A LEU* 3.9 4.9 - - + -
90A LEU* 3.9 15.5 - - + -
101A LEU* 2.9 24.2 + - + +
102A LEU* 3.0 6.5 + - - +
104A TYR* 1.3 77.2 - - + +
106A LEU* 1.3 61.1 + - - +
108A PHE* 3.3 13.6 + - + +
109A HIS* 2.9 42.6 + - + -
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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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87A PHE* 3.4 35.3 - - + -
90A LEU* 3.4 30.7 - - + +
91A ARG* 3.7 25.4 - - + +
94A TYR* 3.6 32.3 - - + -
102A LEU 2.7 15.8 + - - +
103A LEU* 3.6 5.4 - - - +
105A VAL* 1.3 73.6 - - - +
107A HIS* 1.3 58.7 + - - +
109A HIS* 2.7 24.5 + - - +
110A GLY* 3.3 9.4 + - - -
123A PHE* 3.8 31.4 - - + -
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Residues in contact with HIS 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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5A ILE* 3.4 46.9 - - + +
6A ALA* 4.2 8.6 + - - +
58A MET* 5.6 0.4 - - - -
103A LEU 3.1 9.9 + - - +
104A TYR* 2.8 24.1 + + - -
105A VAL 3.3 0.6 - - - -
106A LEU* 1.3 78.5 - - - +
108A PHE* 1.3 103.7 + + - +
109A HIS 3.2 0.7 + - - -
110A GLY 3.5 8.1 + - - +
113A ASN* 3.5 39.0 + - + +
114A MET 5.0 0.7 - - - -
115A ILE* 3.6 31.9 - - + -
123A PHE* 4.5 6.9 - - - -
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Residues in contact with PHE 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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5A ILE* 5.7 1.1 - - + -
67A TRP* 4.1 7.4 - + - -
70A VAL* 4.5 4.7 - - + -
104A TYR* 3.4 61.9 - + - -
105A VAL* 3.3 14.9 + - + +
106A LEU 3.1 0.8 + - - -
107A HIS* 1.3 101.0 + + - +
109A HIS* 1.3 68.4 + + + +
113A ASN* 3.9 7.0 - - - +
130A ARG* 3.3 22.9 - - - +
131A THR 4.0 7.6 - - - +
132A ILE* 3.7 26.7 - - + +
136A SER* 3.4 39.7 - - - -
139A ARG* 5.7 5.6 - - - -
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Residues in contact with HIS 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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74A ILE* 4.5 9.5 - - + +
79A LEU* 3.6 43.5 - - + +
80A SER 4.3 4.5 - - - -
87A PHE* 3.7 19.3 - + + -
90A LEU* 5.0 1.0 - - - +
105A VAL* 2.9 36.0 + - + -
106A LEU* 2.7 14.8 + - - +
108A PHE* 1.3 81.9 - - + +
110A GLY* 1.3 58.5 + - - +
127A PHE* 3.3 14.3 - + + -
128A GLY* 2.9 19.4 + - - -
130A ARG* 3.1 27.9 - - - +
131A THR* 2.7 30.3 + - - -
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Residues in contact with GLY 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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87A PHE* 4.1 7.2 - - - -
106A LEU 3.3 8.6 + - - -
107A HIS 3.5 6.2 + - - -
109A HIS* 1.3 78.0 - - - +
111A PHE* 1.3 57.9 + - - -
112A SER 2.9 1.7 + - - -
113A ASN* 2.7 27.1 + - - -
114A MET 5.1 1.3 - - - -
123A PHE* 5.2 1.3 - - - -
125A THR* 4.0 9.6 - - - -
126A PRO 3.4 10.3 - - - -
128A GLY* 3.4 4.7 - - - -
130A ARG* 3.5 11.1 - - - -
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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