Contacts of the helix formed by residues 99 - 113 (chain A) in PDB entry 1XAI
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASP* 5.0 2.8 + - - -
42A VAL* 4.8 4.0 - - - +
98A GLY* 1.3 81.3 - - - +
100A GLY* 1.3 64.9 + - - -
101A ALA* 3.3 3.8 - - - -
102A THR* 3.2 8.7 + - - +
103A GLY* 3.3 14.9 + - - -
123A PRO* 5.5 0.2 - - - +
124A THR* 3.8 2.0 + - - -
125A THR* 4.0 19.3 - - - -
128A ALA* 4.3 6.6 - - - +
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Residues in contact with GLY 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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71A LYS* 5.6 0.2 - - - -
99A GLY* 1.3 71.6 - - - -
101A ALA* 1.3 60.7 + - - +
103A GLY* 3.2 1.4 + - - -
104A ASP* 2.8 38.5 + - - +
125A THR* 4.4 3.6 - - - +
127A LEU* 4.5 10.9 - - - +
128A ALA* 4.4 3.0 - - - +
131A SER* 3.2 29.9 + - - -
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Residues in contact with ALA 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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67A GLY* 3.2 36.8 - - - +
68A GLU* 3.2 22.6 + - - +
70A THR* 4.4 2.2 - - - -
71A LYS* 3.7 16.3 - - + +
99A GLY* 3.3 1.3 - - - -
100A GLY* 1.3 72.9 - - - +
102A THR* 1.3 67.2 + - - +
103A GLY 2.9 2.6 + - - -
104A ASP 3.2 1.0 + - - -
105A PHE* 3.1 23.2 + - - +
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Residues in contact with THR 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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37A LEU* 5.4 3.9 - - - +
39A ASP* 3.3 48.9 - - + +
64A ILE* 3.7 25.7 - - + +
65A PRO 4.2 1.1 - - - +
67A GLY* 4.2 8.7 - - - +
70A THR* 4.4 1.1 - - + -
96A ALA* 4.3 3.2 - - - +
97A VAL 4.2 2.7 + - - -
98A GLY* 3.2 30.3 + - - -
99A GLY 3.2 6.3 + - - +
101A ALA* 1.3 76.0 - - - +
103A GLY* 1.3 56.1 + - - +
105A PHE* 3.9 0.6 - - - +
106A ALA* 3.0 31.9 + - - +
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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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96A ALA* 4.2 7.6 - - - -
99A GLY 3.3 12.3 + - - -
100A GLY* 3.2 6.7 + - - -
101A ALA 2.9 1.0 - - - -
102A THR* 1.3 76.4 + - - +
104A ASP* 1.3 65.6 + - - +
107A GLY* 3.0 21.7 + - - -
119A PHE* 3.6 7.6 - - - -
121A GLN* 4.0 22.2 - - - +
137A VAL* 4.2 2.2 - - - +
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Residues in contact with ASP 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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71A LYS* 3.2 25.1 + - + -
100A GLY 2.8 22.6 + - - +
101A ALA 3.8 3.4 - - - +
103A GLY* 1.3 72.3 - - - +
105A PHE* 1.3 58.6 + - - +
108A PHE 3.0 18.0 + - - -
131A SER* 4.4 16.0 - - - +
136A LYS 3.4 18.5 - - - +
137A VAL* 3.2 8.3 - - - +
138A GLY 3.0 38.5 + - - +
145A LYS* 4.6 1.9 + - - -
146A ASN* 4.0 11.8 + - - +
115B ARG* 5.5 1.9 + - - -
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Residues in contact with PHE 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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37A LEU* 4.4 1.8 - - + -
64A ILE* 3.4 33.7 - - + -
70A THR* 3.4 44.6 - - + -
71A LYS* 4.1 4.2 - - + +
75A GLN* 3.5 20.4 - - + -
76A TYR* 3.7 25.6 - + + -
79A THR* 3.6 18.8 - - + -
101A ALA 3.1 14.5 + - - +
102A THR 3.9 1.6 - - - +
104A ASP* 1.3 74.4 - - - +
106A ALA* 1.3 76.2 + - - +
107A GLY 2.9 1.3 - - - -
108A PHE* 2.8 16.4 + - - +
109A VAL* 2.9 30.1 + - + +
138A GLY 3.6 6.9 + - - -
139A ILE* 3.9 14.4 - - + -
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Residues in contact with ALA 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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37A LEU* 3.4 35.2 - - + -
94A ILE* 3.7 10.8 - - + +
96A ALA* 3.8 22.2 - - + -
102A THR 3.0 19.8 + - - +
103A GLY 4.2 0.2 - - - +
105A PHE* 1.3 77.5 - - - +
107A GLY* 1.3 57.1 + - - +
109A VAL* 3.4 2.4 + - - +
110A ALA* 2.9 31.2 + - - +
119A PHE* 4.0 2.5 - - + -
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Residues in contact with GLY 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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103A GLY 3.0 9.3 + - - -
105A PHE 2.9 1.2 - - - -
106A ALA* 1.3 75.6 - - - +
108A PHE* 1.3 59.6 + - - +
110A ALA* 3.8 1.2 - - - +
111A ALA* 2.8 31.9 + - - +
119A PHE* 3.2 31.8 - - - -
137A VAL* 3.4 16.7 - - - +
152A TYR* 4.8 1.6 - - - +
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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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76A TYR* 3.4 36.9 - + - -
104A ASP 3.0 12.7 + - - +
105A PHE* 2.8 11.8 + - - +
107A GLY* 1.3 71.2 - - - +
109A VAL* 1.3 61.2 + - - +
111A ALA* 4.2 1.1 - - + -
112A THR* 2.9 36.3 + - + +
137A VAL* 3.5 6.2 - - + +
138A GLY* 3.7 13.2 - - - +
139A ILE* 3.6 38.8 - - + -
148A ILE* 3.5 9.9 - - + -
149A GLY* 3.6 28.7 - - - -
150A ALA* 4.3 4.5 - - + -
76B TYR* 3.4 24.2 - + - -
112B THR* 3.8 13.7 - - + -
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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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37A LEU* 4.3 11.2 - - + -
76A TYR* 4.2 12.8 - - + +
79A THR* 4.5 11.0 - - + -
80A LEU* 3.6 24.6 - - + +
83A ILE* 5.2 4.3 - - + -
94A ILE* 4.9 10.5 - - + -
105A PHE* 2.9 51.2 + - + +
106A ALA* 3.5 9.9 - - - +
108A PHE* 1.3 75.8 - - - +
110A ALA* 1.3 62.3 - - - +
112A THR* 3.1 6.8 + - - -
113A LEU* 2.9 30.4 + - + +
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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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94A ILE* 3.5 30.0 - - + +
106A ALA 2.9 17.5 + - - +
107A GLY 3.8 3.8 - - - +
109A VAL* 1.3 79.3 - - - +
111A ALA* 1.3 59.6 + - - +
112A THR 3.2 1.2 + - - -
113A LEU* 3.6 3.1 + - - -
117A VAL* 3.0 39.0 + - + +
118A HIS 4.2 0.4 - - - +
119A PHE* 4.1 22.9 - - + -
152A TYR* 4.0 2.0 + - - -
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Residues in contact with ALA 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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107A GLY 2.8 19.7 + - - +
108A PHE* 4.1 8.1 - - + +
109A VAL 3.2 0.2 - - - -
110A ALA* 1.3 75.5 - - - +
112A THR* 1.3 64.2 + - + +
115A ARG 3.9 4.0 - - - +
116A GLY* 3.6 14.2 + - - -
137A VAL* 4.4 4.7 - - + -
150A ALA* 4.8 8.5 - - + -
152A TYR* 3.4 45.2 - - + -
149B GLY 4.0 2.4 - - - +
150B ALA* 4.6 5.2 - - - +
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Residues in contact with THR 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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76A TYR* 2.5 30.6 + - - +
80A LEU* 4.0 2.1 - - - +
108A PHE* 2.9 37.9 + - + +
109A VAL 3.1 4.9 + - - -
111A ALA* 1.3 82.2 - - + +
113A LEU* 1.3 66.0 + - - +
114A LEU 3.2 1.4 + - - -
115A ARG 3.2 1.9 + - - -
150A ALA* 5.8 1.8 - - + -
108B PHE* 3.8 16.8 - - + -
112B THR* 4.8 2.2 - - + -
148B ILE* 3.3 12.2 - - - +
149B GLY 3.0 35.6 + - - +
150B ALA* 5.2 2.7 - - + -
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Residues in contact with LEU 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* 3.6 24.9 - - + -
83A ILE* 3.9 24.2 - - + -
84A LEU* 3.7 28.9 - - + -
88A VAL* 4.4 10.1 - - + -
92A THR* 4.9 8.5 - - + -
94A ILE* 4.7 10.5 - - + -
109A VAL* 2.9 17.6 + - + +
110A ALA 3.6 3.5 + - - +
112A THR* 1.3 72.0 + - - +
114A LEU* 1.3 63.1 + - + +
115A ARG 3.0 0.9 - - - -
116A GLY 2.7 23.2 + - - -
117A VAL* 3.0 45.2 - - + +
147B LEU 4.2 2.5 - - - +
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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