Contacts of the strand formed by residues 94 - 103 (chain H) in PDB entry 1LP9
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 THR 94 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H THR* 4.1 12.3 - - + -
11H SER 3.5 8.3 - - - +
12H VAL* 4.0 14.5 - - + +
93H HIS* 1.3 76.4 + - - +
95H VAL* 1.3 67.2 + - - +
96H GLN* 3.9 26.9 - - + +
117H ALA 3.8 0.3 - - - +
118H TYR* 3.2 7.9 - - - -
119H ASP* 2.7 42.0 + - - -
31I HIS* 4.2 15.9 - - + -
32I PRO* 4.5 13.3 - - - +
33I SER* 5.0 0.9 + - - -
62I PHE* 4.1 10.8 - - + -
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H PHE 3.9 0.5 - - - +
10H THR* 3.6 2.4 - - - -
11H SER* 2.9 46.3 + - - +
74H HIS* 5.0 10.7 + - + +
77H ASP* 4.6 9.2 - - + -
78H LEU* 3.7 31.4 - - + +
81H LEU* 4.4 10.1 - - + -
94H THR* 1.3 74.9 - - - +
96H GLN* 1.3 66.8 + - - +
116H TYR* 4.1 27.4 - - + -
117H ALA 3.5 5.6 - - - +
118H TYR* 4.0 15.7 - - + -
9J LEU* 4.6 6.5 - - + -
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Residues in contact with GLN 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE 3.2 7.0 - - - +
10H THR* 4.3 1.8 - - - +
94H THR* 3.9 11.3 - - + +
95H VAL* 1.3 79.8 - - - +
97H ARG* 1.3 62.3 + - - +
116H TYR* 3.1 9.2 - - - +
117H ALA* 2.8 36.1 + - + +
120H GLY* 4.2 5.9 + - - -
31I HIS* 2.8 25.8 + - - -
56I PHE* 3.2 34.9 - - + -
60I TRP* 2.9 48.4 + - + +
62I PHE* 3.3 18.4 - - + -
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Residues in contact with ARG 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 2.8 46.3 + - + -
70H HIS* 3.4 28.9 + - - +
73H THR* 5.9 1.4 - - - +
74H HIS* 3.5 29.5 + - + -
95H VAL* 5.4 0.4 - - + -
96H GLN* 1.3 77.6 - - - +
98H MET* 1.3 67.8 + - - +
99H TYR* 3.7 12.5 - - - -
114H HIS* 2.9 30.1 + - - +
115H GLN 3.2 11.4 - - - +
116H TYR* 2.9 39.5 + - + -
56I PHE* 3.4 7.1 - - - -
60I TRP* 4.2 1.3 - - - -
3J TRP* 3.7 22.0 - - - -
5J PHE 4.8 0.4 + - - -
6J PHE* 5.8 1.8 - - - +
7J PRO* 3.9 14.7 + - - +
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Residues in contact with MET 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG* 3.5 30.1 - - - +
7H TYR 3.2 14.4 - - - +
8H PHE* 3.7 29.4 - - + -
97H ARG* 1.3 77.5 - - - +
99H TYR* 1.3 86.8 + - - +
113H TYR* 3.8 20.9 - - + -
114H HIS* 3.4 0.3 - - - -
115H GLN* 2.9 51.0 + - + +
56I PHE* 4.2 7.4 - - + -
58I LYS* 3.7 28.9 - - + +
60I TRP* 4.3 5.4 - - + -
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Residues in contact with TYR 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ARG* 3.5 2.6 - - - -
7H TYR* 2.9 44.0 + + + +
9H PHE* 3.6 20.9 - + - -
70H HIS* 2.8 37.0 - + - -
97H ARG* 3.7 31.9 - - - -
98H MET* 1.3 81.7 - - - +
100H GLY* 1.3 58.5 + - - +
113H TYR 3.2 16.4 - - - +
114H HIS* 3.8 13.7 - + + -
156H LEU* 5.4 0.7 - - + -
159H TYR* 3.4 41.5 - + - -
160H LEU* 5.1 2.0 - - + -
2J LEU* 3.3 6.5 - - + +
3J TRP* 2.9 25.9 + + + +
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Residues in contact with GLY 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H MET* 3.1 13.0 - - - -
6H ARG* 4.0 7.6 - - - -
7H TYR* 5.9 1.1 - - - -
98H MET* 4.3 0.8 - - - -
99H TYR* 1.3 82.4 - - - +
101H CYS* 1.3 59.8 + - - -
112H GLY* 3.2 3.5 - - - -
113H TYR* 2.8 32.4 + - - -
160H LEU* 3.5 9.3 - - - +
164H CYS* 3.9 10.8 - - - -
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Residues in contact with CYS 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H SER* 3.2 4.2 - - - -
5H MET* 3.0 34.3 + - - -
6H ARG* 3.3 3.7 + - - +
100H GLY* 1.3 73.9 - - - +
102H ASP* 1.3 63.4 + - - +
103H VAL* 5.3 0.2 - - - -
109H PHE* 4.2 8.1 - - + -
111H ARG 3.2 9.4 - - - +
112H GLY* 4.3 0.2 - - - -
113H TYR* 4.9 0.2 - - - -
160H LEU 3.7 16.8 - - - +
164H CYS* 2.1 57.7 - - - -
165H VAL* 3.7 8.7 - - + -
168H LEU* 4.5 7.4 - - - +
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Residues in contact with ASP 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H HIS 3.4 6.3 - - - +
4H SER* 3.4 8.3 - - - -
6H ARG* 2.8 32.4 + - - -
101H CYS* 1.3 73.6 - - - +
103H VAL* 1.3 67.2 + - - +
109H PHE* 3.8 3.3 - - - -
110H LEU* 2.9 33.8 + - + -
111H ARG* 2.7 24.9 + - - +
113H TYR* 2.6 29.2 + - - -
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Residues in contact with VAL 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H SER* 3.5 5.9 - - - -
3H HIS* 2.8 48.5 + - + +
101H CYS* 5.3 0.4 - - - -
102H ASP* 1.3 80.4 - - - +
104H GLY* 1.3 66.5 + - - +
107H TRP* 3.7 32.5 - - + +
108H ARG 3.2 15.0 - - - +
110H LEU* 3.8 5.9 - - - +
165H VAL* 4.0 25.4 - - + +
168H LEU* 3.7 23.6 - - + -
169H ARG* 5.6 1.8 - - + +
172H LEU* 4.9 1.8 - - + -
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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