Contacts of the helix formed by residues 99 - 113 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASP* 5.1 2.6 + - - -
42B VAL* 4.8 4.0 - - - +
98B GLY* 1.3 81.3 - - - +
100B GLY* 1.3 64.2 + - - -
101B ALA* 3.3 3.6 - - - -
102B THR* 3.3 8.9 + - - +
103B GLY* 3.3 14.7 + - - -
124B THR* 3.9 2.2 + - - -
125B THR* 4.0 19.1 - - - -
128B ALA* 4.3 6.3 - - - +
131B SER* 4.6 0.2 + - - -
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY* 1.3 71.0 - - - -
101B ALA* 1.3 59.9 + - - +
103B GLY* 3.2 2.3 + - - -
104B ASP* 2.8 38.7 + - - +
125B THR* 4.4 3.6 - - - +
127B LEU* 4.5 11.3 - - - +
128B ALA* 4.4 3.4 - - - +
131B SER* 3.1 30.2 + - - -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLY* 3.2 36.8 - - - +
68B GLU* 3.3 22.6 + - - +
70B THR* 4.4 2.0 - - - -
71B LYS* 3.8 16.6 - - + +
99B GLY* 3.3 1.3 - - - -
100B GLY* 1.3 73.5 - - - +
102B THR* 1.3 67.0 + - - +
103B GLY 2.9 2.2 + - - -
104B ASP* 3.2 1.4 + - - -
105B PHE* 3.1 23.2 + - - +
145B LYS* 6.1 0.4 - - - +
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 5.4 3.4 - - - -
38B ILE 5.2 0.7 - - - -
39B ASP* 3.3 48.0 - - + +
64B ILE* 3.7 26.1 - - + +
65B PRO 4.2 5.8 - - - +
67B GLY* 4.3 4.0 - - - +
70B THR* 4.4 1.6 - - + -
96B ALA* 4.4 2.5 - - - +
97B VAL 4.9 2.8 + - - -
98B GLY* 3.2 30.8 + - - -
99B GLY* 3.3 6.2 + - - +
101B ALA* 1.3 78.6 - - - +
103B GLY* 1.3 56.7 + - - +
105B PHE* 3.9 0.7 - - - +
106B ALA* 3.0 32.2 + - - +
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA* 4.2 6.5 - - - -
99B GLY 3.3 12.8 + - - -
100B GLY* 3.2 6.9 + - - -
101B ALA 2.9 1.0 - - - -
102B THR* 1.3 77.2 + - - +
104B ASP* 1.3 65.0 + - - +
107B GLY* 3.0 18.7 + - - -
119B PHE* 3.5 11.7 - - - -
121B GLN* 4.0 22.7 - - - -
131B SER* 5.8 0.7 - - - -
137B VAL* 4.2 1.4 - - - +
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ARG* 5.4 1.7 + - - -
71B LYS* 3.3 24.6 + - + -
100B GLY 2.8 23.1 + - - +
101B ALA 3.2 3.8 + - - +
103B GLY* 1.3 72.6 - - - +
105B PHE* 1.3 57.4 + - - +
108B PHE* 3.0 17.8 + - - +
121B GLN* 5.8 0.3 + - - -
131B SER* 4.5 15.5 - - - +
136B LYS 3.4 19.5 - - - +
137B VAL* 3.2 9.1 - - - +
138B GLY 3.0 39.0 + - - +
145B LYS* 4.6 2.4 + - - -
146B ASN* 4.0 11.2 + - - +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 4.5 1.6 - - + -
64B ILE* 3.4 45.3 - - + -
70B THR* 3.5 33.0 - - + -
71B LYS* 4.2 4.5 - - + -
75B GLN* 3.6 12.6 - - + -
76B TYR* 3.7 26.2 - + + -
79B THR* 3.5 25.6 - - + -
101B ALA 3.1 14.7 + - - +
102B THR 3.9 2.0 - - - +
104B ASP* 1.3 74.0 - - - +
106B ALA* 1.3 75.1 + - - +
107B GLY 2.9 1.6 - - - -
108B PHE* 2.8 16.4 + - - +
109B VAL* 2.9 31.3 + - + +
138B GLY 3.6 6.6 + - - -
139B ILE* 4.0 13.7 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.4 37.0 - - + -
94B ILE* 3.7 10.9 - - + +
96B ALA* 3.8 22.9 - - + -
102B THR 3.0 17.3 + - - +
105B PHE* 1.3 80.3 - - + +
107B GLY* 1.3 57.4 + - - +
109B VAL* 3.3 3.1 + - - +
110B ALA* 2.8 30.7 + - - +
119B PHE* 3.9 2.0 - - + -
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLY 3.0 8.7 + - - -
105B PHE 2.9 1.4 - - - -
106B ALA* 1.3 76.8 - - - +
108B PHE* 1.3 59.0 + - - +
110B ALA* 3.8 1.2 - - - +
111B ALA* 2.8 31.7 + - - +
119B PHE* 3.2 32.2 - - - -
137B VAL* 3.4 16.8 - - - +
152B TYR* 4.7 2.1 - - - -
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Residues in contact with PHE 108 (chain B).
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* 3.5 22.2 - + - -
112A THR* 3.8 6.5 - - + -
76B TYR* 3.4 37.8 - + - -
104B ASP 3.0 12.3 + - - +
105B PHE* 2.8 12.2 + - - +
107B GLY* 1.3 70.5 - - - +
109B VAL* 1.3 61.7 + - - +
111B ALA* 3.8 1.3 - - + -
112B THR* 2.8 41.2 + - + +
137B VAL* 3.5 6.2 - - + +
138B GLY* 3.7 13.2 - - - +
139B ILE* 3.6 38.8 - - + -
148B ILE* 3.6 11.0 - - + -
149B GLY* 3.5 30.3 - - - -
150B ALA* 4.3 5.2 - - + -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 4.4 11.2 - - + -
76B TYR* 4.2 12.6 - - + +
79B THR* 4.5 11.0 - - + -
80B LEU* 3.6 23.9 - - + +
83B ILE* 5.1 4.7 - - + -
94B ILE* 4.7 11.0 - - + -
105B PHE* 2.9 49.9 + - + +
106B ALA* 3.4 11.0 - - - +
108B PHE* 1.3 77.3 - - - +
110B ALA* 1.3 59.4 + - - +
112B THR* 3.1 7.4 + - - -
113B LEU* 2.9 30.7 + - + +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.5 31.4 - - + -
106B ALA 2.8 17.9 + - - +
107B GLY 3.8 3.6 - - - +
109B VAL* 1.3 78.5 - - - +
111B ALA* 1.3 58.4 + - - +
112B THR 3.2 0.7 + - - -
113B LEU* 3.6 2.7 + - - -
117B VAL* 3.0 38.1 + - + +
118B HIS 4.2 0.4 - - - +
119B PHE* 4.0 22.9 - - + -
152B TYR* 4.4 2.5 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLY 4.0 2.3 - - - +
150A ALA* 4.6 5.2 - - - +
107B GLY 2.8 24.0 + - - +
108B PHE* 4.1 7.9 - - - +
109B VAL 3.2 0.2 - - - -
110B ALA* 1.3 73.2 - - - +
112B THR* 1.3 63.8 + - + +
115B ARG 3.8 3.8 - - - +
116B GLY* 3.6 14.6 + - - -
137B VAL* 4.4 4.5 - - + -
150B ALA* 4.8 9.4 - - + -
152B TYR* 3.4 43.8 - - + -
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Residues in contact with THR 112 (chain B).
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* 3.8 16.6 - - + -
112A THR* 4.8 2.7 - - + -
148A ILE* 3.3 9.9 - - - -
149A GLY 3.0 36.0 + - - +
150A ALA* 5.2 2.5 - - + -
76B TYR* 2.6 33.1 + - - +
80B LEU* 4.0 3.8 - - - +
108B PHE* 2.8 37.6 + - + +
109B VAL* 3.1 5.6 + - - -
111B ALA* 1.3 83.1 - - + +
113B LEU* 1.3 66.5 + - - +
114B LEU 3.2 1.2 + - - -
115B ARG 3.2 2.9 + - - -
150B ALA* 5.8 1.6 - - + -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU 4.3 2.2 - - - +
80B LEU* 3.6 23.3 - - + -
83B ILE* 4.0 23.8 - - + -
84B LEU* 3.6 30.3 - - + -
88B VAL* 4.4 11.7 - - + -
92B THR* 4.9 8.3 - - + -
94B ILE* 4.7 9.6 - - + -
109B VAL* 2.9 17.8 + - + +
110B ALA 3.6 3.3 + - - +
112B THR* 1.3 72.8 - - - +
114B LEU* 1.3 63.3 + - + +
115B ARG 3.0 0.4 - - - -
116B GLY 2.6 23.2 + - - -
117B VAL* 3.0 45.5 - - + +
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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