Contacts of the helix formed by residues 98 - 115 (chain A) in PDB entry 2W99
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 ARG 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 4.0 6.8 - - + +
95A LYS* 2.6 55.7 + - - +
97A SER* 1.3 85.5 + - - +
99A LEU* 1.3 60.1 + - - -
100A GLN 3.6 1.1 - - - -
101A LEU* 3.4 32.0 - - + +
102A LEU* 3.3 17.7 + - - +
139A GLN* 5.2 10.1 - - - +
140A MET* 4.2 26.8 - - + +
143A LEU* 5.7 5.9 - - - +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.3 21.1 - - + -
56A MET* 3.7 30.5 - - + -
57A ARG* 3.9 4.3 - - - +
60A VAL* 3.0 32.7 - - + +
85A LEU* 4.7 6.7 - - + -
89A LEU* 4.3 24.2 - - + -
94A VAL* 4.3 4.3 - - + -
95A LYS 3.3 2.9 + - - +
96A LYS* 2.8 19.0 + - + +
98A ARG* 1.3 74.3 - - - +
100A GLN* 1.3 59.0 + - - +
101A LEU 3.0 1.8 - - - -
102A LEU* 2.6 38.0 + - + +
103A GLY* 2.9 9.9 + - - -
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.8 14.5 - - + +
63A TRP* 4.0 37.6 + - + -
96A LYS 4.4 2.0 + - - -
97A SER 4.9 4.4 + - - +
98A ARG 3.6 0.4 - - - -
99A LEU* 1.3 77.6 - - - +
101A LEU* 1.3 62.5 + - - +
103A GLY* 3.2 1.9 + - - -
104A ALA* 2.9 23.2 + - - +
128A THR* 3.4 35.5 + - + +
131A SER* 3.8 17.4 + - - -
132A ILE* 4.1 6.0 - - + +
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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
----------------------------------------------------------
97A SER 5.2 1.9 + - - +
98A ARG* 3.4 42.7 + - + +
99A LEU 3.0 0.8 - - - -
100A GLN* 1.3 79.5 - - - +
102A LEU* 1.3 57.5 + - - +
104A ALA* 3.4 1.2 - - - +
105A THR* 3.0 31.9 + - - -
132A ILE* 3.5 40.0 - - + +
136A GLU* 4.1 23.6 - - + +
137A LEU* 4.0 25.6 - - - +
140A MET* 3.6 23.1 - - + -
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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
----------------------------------------------------------
85A LEU* 4.4 14.8 - - + +
88A PHE* 3.7 33.7 - - + -
89A LEU* 3.2 36.1 - - + -
94A VAL* 4.5 5.4 - - + -
98A ARG 3.3 8.7 + - - +
99A LEU* 2.6 24.4 + - + +
101A LEU* 1.3 71.5 - - - +
103A GLY* 1.3 66.5 + - - +
105A THR* 3.2 3.7 + - - +
106A CYS* 2.9 43.1 + - - -
140A MET* 4.2 18.4 - - + -
144A LEU* 4.5 8.5 - - + -
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Residues in contact with GLY 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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60A VAL* 4.0 9.6 - - - -
63A TRP* 4.3 3.1 - - - -
64A MET* 3.6 29.9 - - - +
85A LEU* 4.2 7.4 - - - +
99A LEU 2.9 11.3 + - - -
100A GLN 3.2 3.3 + - - -
102A LEU* 1.3 77.6 - - - +
104A ALA* 1.3 64.1 + - - +
106A CYS* 2.9 10.8 + - - +
107A MET* 3.0 13.2 + - - +
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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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63A TRP* 3.8 14.0 - - + -
100A GLN 2.9 12.9 + - - +
101A LEU 3.4 9.0 - - - +
103A GLY* 1.3 75.0 - - - +
105A THR* 1.3 58.1 + - - +
107A MET* 3.2 15.9 + - - +
108A PHE* 2.8 27.4 + - - +
124A LEU* 3.7 10.7 - - + +
128A THR* 5.2 0.7 - - + -
132A ILE* 3.8 12.3 - - + -
137A LEU* 3.5 22.2 - - + -
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Residues in contact with THR 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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101A LEU* 3.0 19.0 + - - +
102A LEU* 3.2 6.9 + - - -
104A ALA* 1.3 75.0 - - - +
106A CYS* 1.3 63.5 + - - +
108A PHE* 2.9 10.6 + - + +
109A VAL* 2.9 22.9 + - + +
137A LEU* 3.8 12.9 + - - +
140A MET* 3.0 24.5 - - - +
141A GLU* 3.3 41.5 - - + +
144A LEU* 3.7 16.6 - - + -
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Residues in contact with CYS 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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64A MET* 4.4 2.5 - - + -
81A ALA* 3.2 24.5 - - + +
84A TYR* 3.7 15.7 - - + -
85A LEU* 3.5 35.0 - - - -
102A LEU* 2.9 27.8 + - - -
103A GLY 3.4 7.4 - - - +
105A THR* 1.3 76.5 - - - +
107A MET* 1.3 57.2 + - - +
110A ALA* 2.8 30.5 + - - +
144A LEU* 3.7 21.3 - - - -
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Residues in contact with MET 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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63A TRP* 3.6 30.5 - - + -
64A MET* 3.7 39.7 - - + +
67A VAL* 4.1 13.5 - - + -
68A CYS* 3.9 17.0 - - - -
77A VAL* 4.4 4.2 - - + +
78A PHE* 5.5 0.7 - - - -
81A ALA* 3.9 17.0 - - + -
103A GLY 3.0 5.3 + - - -
104A ALA* 3.6 7.2 - - - +
106A CYS* 1.3 73.9 - - - +
108A PHE* 1.3 59.5 + - - +
110A ALA* 4.0 2.5 - - - -
111A SER* 2.8 35.2 + - - -
119A LEU* 4.4 6.1 - - + -
124A LEU* 3.4 30.1 - - + -
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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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104A ALA 2.8 16.9 + - - +
105A THR* 2.9 13.9 + - + +
107A MET* 1.3 73.4 - - - +
109A VAL* 1.3 57.5 + - - +
111A SER* 3.9 2.9 - - - -
112A LYS* 2.8 42.0 + - + +
119A LEU* 3.5 22.4 - - - -
121A ALA* 3.6 11.2 - - + -
124A LEU* 3.6 22.1 - - + +
137A LEU* 3.7 13.0 - - + -
138A LEU* 3.9 13.0 - - + -
141A GLU* 3.6 38.6 - - + -
44B GLU* 3.3 52.3 - - + -
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Residues in contact with VAL 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 TYR* 3.5 23.6 - - + +
105A THR 2.9 15.6 + - - +
106A CYS 4.1 0.7 - - - +
108A PHE* 1.3 73.9 - - + +
110A ALA* 1.3 67.2 + - - +
112A LYS* 3.3 8.0 + - + +
113A MET* 3.0 25.3 + - + +
141A GLU* 3.5 38.6 - - + +
144A LEU* 4.2 11.2 - - + -
145A VAL* 4.0 12.8 - - + -
152A LEU* 4.2 24.9 - - + -
54B VAL* 5.7 5.2 - - + -
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Residues in contact with ALA 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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77A VAL* 3.4 31.6 - - + +
80A LEU* 4.1 11.9 - - + -
81A ALA* 3.8 13.9 - - + +
84A TYR* 3.7 8.9 - - + -
106A CYS 2.8 23.9 + - - +
107A MET 3.8 2.9 - - - +
109A VAL* 1.3 73.5 - - - +
111A SER* 1.3 61.9 + - - +
113A MET* 3.0 13.5 + - - +
114A LYS* 3.0 17.7 + - - +
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Residues in contact with SER 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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77A VAL* 3.8 7.1 - - - +
107A MET 2.8 21.3 + - - -
108A PHE 3.9 2.7 - - - -
110A ALA* 1.3 70.0 - - - +
112A LYS* 1.3 61.7 + - - +
113A MET 3.0 0.2 + - - -
115A GLU* 2.8 60.2 + - - +
118A PRO* 3.3 3.6 - - - +
119A LEU* 2.8 42.7 + - - +
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Residues in contact with LYS 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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108A PHE* 2.8 40.4 + - + +
109A VAL* 3.3 8.3 + - - +
111A SER* 1.3 76.0 + - - +
113A MET* 1.3 53.0 + - - +
118A PRO* 3.9 19.5 - - + -
141A GLU* 2.7 28.5 + - - -
44B GLU* 3.1 18.4 + - + +
49B LEU 2.7 27.2 + - - -
51B ILE* 3.0 30.0 - - + +
54B VAL* 4.2 17.9 - - + -
55B ARG* 2.3 41.3 + - - -
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Residues in contact with MET 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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80A LEU* 4.3 11.7 - - + -
84A TYR* 3.8 14.6 - - - +
109A VAL* 3.0 23.4 + - + +
110A ALA 3.4 8.5 - - - +
111A SER 3.0 0.4 - - - -
112A LYS* 1.3 79.3 - - - +
114A LYS* 1.3 68.5 + - + +
115A GLU 3.8 0.2 - - - -
152A LEU* 4.1 7.2 - - + +
153A ALA* 3.7 33.4 - - + +
54B VAL* 4.0 17.0 - - + +
55B ARG* 4.1 25.5 + - + +
58B ALA* 3.8 25.1 - - + -
59B LEU* 5.5 2.9 - - + -
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Residues in contact with LYS 114 (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 GLU* 4.3 15.5 - - + +
76A GLU* 3.7 48.0 - - + +
77A VAL* 4.0 16.6 - - + -
80A LEU* 3.7 32.6 - - + +
110A ALA 3.0 9.4 + - - +
113A MET* 1.3 89.9 + - - +
115A GLU* 1.3 63.0 + - - +
116A THR* 4.3 0.9 + - - +
153A ALA* 5.2 2.4 - - - +
154A ALA 4.5 12.2 + - - -
156A THR* 4.8 7.9 - - - -
159A ASP* 5.2 5.5 + - - -
55B ARG* 4.9 0.4 - - - -
62B ARG* 4.8 11.3 - - - +
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Residues in contact with GLU 115 (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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72A LYS 4.8 1.0 - - - +
73A CYS* 3.2 27.0 - - - +
74A GLU* 3.4 30.0 + - + +
77A VAL* 3.8 14.2 - - + +
111A SER* 2.8 38.0 + - - +
113A MET 3.8 0.6 - - - -
114A LYS* 1.3 82.4 - - - +
116A THR* 1.3 64.7 + - - +
117A ILE 3.5 19.9 + - - +
118A PRO* 3.8 8.1 - - - +
119A LEU* 4.2 2.6 - - - +
55B ARG* 3.2 20.9 + - - +
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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
------------------------------------------------------------
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