Contacts of the strand formed by residues 94 - 105 (chain A) in PDB entry 1XZ0
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 PHE 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A SER* 3.8 0.9 - - - -
18A PHE* 3.0 74.5 + + + -
81A ILE* 4.2 10.5 - - + -
82A ARG* 5.8 0.2 - - - -
85A ALA* 4.5 10.3 - - + -
90A PHE* 3.9 30.1 - + + -
91A GLU 3.5 21.8 - - - +
92A TYR* 4.4 16.6 - + - -
93A PRO* 1.3 76.6 - - - +
95A GLU* 1.3 68.7 + - - +
96A ILE* 4.0 11.9 - - + -
118A TYR* 3.8 18.6 - + + -
119A GLN* 3.2 21.8 - - - +
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Residues in contact with GLU 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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15A ILE* 5.5 1.8 - - + -
16A ALA 3.5 3.8 - - - +
17A SER* 3.1 30.2 + - - +
94A PHE* 1.3 75.9 - - - +
96A ILE* 1.3 71.9 + - - +
97A GLN* 5.3 3.4 - - + +
118A TYR* 3.8 3.1 - - - -
119A GLN* 3.2 28.1 + - - +
31B HIS* 3.8 17.2 + - + +
32B PRO* 3.7 11.8 - - - +
33B SER* 2.7 34.1 + - - -
34B ASP* 4.3 3.1 + - - +
62B PHE* 3.1 33.1 - - - -
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Residues in contact with ILE 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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14A TRP* 3.8 13.8 - - + +
15A ILE* 3.8 1.9 - - - +
16A ALA* 2.9 42.1 + - + +
18A PHE* 4.5 3.6 - - + -
81A ILE* 4.5 28.0 - - + -
90A PHE* 4.7 12.6 - - + -
94A PHE* 4.0 19.1 - - + -
95A GLU* 1.3 80.6 - - - +
97A GLN* 1.3 71.6 + - - +
98A VAL* 4.6 0.9 - - + -
116A LEU* 4.2 23.3 - - + -
117A ALA 3.5 12.1 - - - +
118A TYR* 4.0 21.1 - - + -
123A PHE* 6.3 0.2 - - + -
144A PHE* 6.2 2.2 - - + -
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Residues in contact with GLN 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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14A TRP 3.5 7.0 - - - +
15A ILE* 5.1 3.4 - - + -
95A GLU* 5.3 4.5 - - + +
96A ILE* 1.3 79.9 - - - +
98A VAL* 1.3 64.6 + - - +
116A LEU* 3.4 4.3 - - - +
117A ALA* 2.9 38.1 + - + +
120A GLY* 4.2 9.4 + - - -
31B HIS* 2.8 29.3 + - - -
56B PHE* 3.2 36.7 - - + -
60B TRP* 3.2 39.1 + - + +
62B PHE* 3.6 18.8 - - + -
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Residues in contact with VAL 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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12A VAL 4.5 0.2 - - - -
13A ILE* 3.3 5.1 - - - -
14A TRP* 3.0 63.2 + - + -
96A ILE* 4.6 1.3 - - + -
97A GLN* 1.3 80.7 - - - +
99A THR* 1.3 65.5 + - - +
114A LEU* 3.5 29.2 - - + -
115A GLN 3.4 9.4 - - - +
116A LEU* 3.9 17.3 - - + -
131A TRP* 6.1 0.9 - - + -
601A JH0 3.9 29.2 - - + +
56B PHE* 3.6 8.1 - - - -
60B TRP* 4.7 1.1 - - - -
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Residues in contact with THR 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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11A HIS* 3.5 28.1 - - - +
12A VAL 3.4 6.5 - - - -
13A ILE* 4.4 1.1 - - - -
98A VAL* 1.3 81.0 - - - +
100A GLY* 1.3 60.5 + - - +
113A PHE* 4.1 10.9 - - + -
114A LEU* 3.4 2.6 - - - +
115A GLN* 3.0 36.4 + - + +
56B PHE* 4.3 15.2 - - + -
60B TRP* 4.0 21.1 - - + -
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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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11A HIS* 3.2 1.9 - - - -
12A VAL* 2.9 37.6 + - - +
98A VAL* 4.9 0.2 - - - +
99A THR* 1.3 77.1 + - - +
101A GLY* 1.3 58.0 + - - -
113A PHE* 3.3 22.0 - - - -
114A LEU* 4.1 10.5 - - - +
601A JH0 4.3 13.5 - - - +
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Residues in contact with GLY 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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10A PHE* 3.3 11.9 - - - -
11A HIS* 4.3 0.4 - - - -
100A GLY* 1.3 74.5 - - - -
102A CYS* 1.3 63.9 + - - +
112A SER* 3.3 4.7 - - - -
113A PHE* 3.1 33.7 + - - +
162A LEU* 4.4 5.8 - - - +
166A CYS* 3.7 18.2 - - - -
601A JH0 4.5 4.3 - - - -
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Residues in contact with CYS 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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9A SER* 3.3 5.3 - - - -
10A PHE* 2.9 31.3 + - - -
101A GLY* 1.3 75.0 - - - +
103A GLU* 1.3 63.4 + - - +
109A VAL* 4.9 6.5 - - + -
111A GLY 3.1 18.6 - - - +
112A SER* 3.7 9.9 - - - -
113A PHE* 3.9 7.5 - - - -
162A LEU 5.2 0.4 - - - +
166A CYS* 3.5 42.2 - - + -
167A PRO* 4.0 12.1 - - + -
170A ILE* 4.0 12.9 - - - +
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Residues in contact with GLU 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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7A PRO 4.0 7.3 - - - +
8A LEU 3.6 13.2 - - - +
9A SER* 3.9 9.7 - - - +
102A CYS* 1.3 79.3 - - - +
104A LEU* 1.3 69.8 + - - +
105A HIS* 2.9 25.9 + - + -
109A VAL* 3.6 6.9 - - - +
110A SER* 2.9 37.4 + - - -
111A GLY* 3.1 11.5 + - - +
113A PHE* 3.8 20.7 - - - -
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Residues in contact with LEU 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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7A PRO* 3.4 24.6 - - - +
8A LEU* 3.1 24.3 + - + +
103A GLU* 1.3 81.0 - - - +
105A HIS* 1.3 65.7 + - - +
106A SER 4.1 1.0 + - - -
107A GLY* 3.6 32.3 - - - +
108A LYS 3.3 17.0 - - - +
109A VAL* 3.8 7.6 - - + +
170A ILE* 3.6 41.3 - - + -
171A LEU* 3.7 22.9 - - + -
174A LEU* 4.8 10.5 - - + -
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Residues in contact with HIS 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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7A PRO* 4.7 10.1 + - + +
103A GLU* 2.9 27.5 + - + -
104A LEU* 1.3 79.5 - - - +
106A SER* 1.3 74.2 + - - +
107A GLY 3.4 0.2 - - - -
108A LYS* 3.1 18.1 + - - +
110A SER* 3.2 25.5 + - - +
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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