Contacts of the strand formed by residues 104 - 118 (chain L) in PDB entry 1S9C
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 104 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L TYR 3.7 0.9 - - - +
21L ALA* 2.9 24.2 - - - -
22L TYR* 2.8 21.1 + - - -
101L PRO* 5.0 4.5 - - - -
103L ALA* 1.3 76.6 - - - +
105L LYS* 1.3 64.1 + - - -
106L LEU* 5.0 1.6 - - - -
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Residues in contact with LYS 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L SER* 6.0 3.4 - - - -
20L TYR 3.3 3.8 - - - +
21L ALA* 3.5 23.1 - - + -
104L GLY* 1.3 73.2 - - - -
106L LEU* 1.3 74.6 + - - +
132L SER* 3.5 16.5 - - - +
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Residues in contact with LEU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L SER* 3.0 30.2 - - - -
20L TYR 2.8 17.0 + - - +
22L TYR* 4.2 14.4 - - + +
64L ILE* 3.6 43.5 - - + -
100L LEU* 5.4 2.7 - - + -
101L PRO* 5.5 4.3 - - + -
104L GLY* 5.0 1.3 - - - -
105L LYS* 1.3 79.8 - - - +
107L LYS* 1.3 58.8 + - - +
108L CYS* 4.7 1.6 - - - -
130L SER* 4.5 14.1 - - - -
131L TYR* 2.8 36.6 - - - +
132L SER* 3.2 13.7 - - - +
137L ILE* 3.6 19.7 - - + -
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Residues in contact with LYS 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L PRO* 5.0 11.2 - - + -
18L PHE 3.8 4.5 - - - +
19L SER* 4.5 3.8 - - - +
106L LEU* 1.3 72.6 - - - +
108L CYS* 1.3 65.9 + - - +
109L GLU* 3.2 30.7 + - - +
129L TYR 3.4 3.6 - - - +
130L SER* 3.5 0.9 - - - -
131L TYR* 3.1 41.5 + - + +
132L SER 4.8 3.5 + - - +
133L GLU 5.6 4.9 - - - +
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Residues in contact with CYS 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L PRO* 3.2 30.3 - - - +
18L PHE* 2.8 58.7 + - + +
20L TYR 4.8 3.1 - - - -
64L ILE* 4.1 13.0 - - - -
106L LEU 4.5 7.2 - - - -
107L LYS* 1.3 77.2 - - - +
109L GLU* 1.3 65.1 + - - +
110L ALA 4.2 0.2 - - - -
128L VAL* 4.2 6.1 - - + -
129L TYR 3.2 6.7 - - - +
130L SER* 3.5 24.0 - - - -
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Residues in contact with GLU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LYS* 6.2 2.0 - - + -
15L LEU 5.2 1.6 - - - +
17L PRO* 4.5 9.9 - - + -
107L LYS* 3.2 33.5 + - + +
108L CYS* 1.3 80.5 - - - +
110L ALA* 1.3 63.0 + - - +
111L VAL* 4.8 6.0 - - + +
127L ASP 3.6 0.5 - - - +
128L VAL* 3.2 4.9 - - - -
129L TYR* 3.2 37.4 + - + +
131L TYR* 4.2 25.2 + - + -
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Residues in contact with ALA 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LYS* 3.5 3.1 - - - +
15L LEU* 3.1 54.4 + - + +
16L PRO 5.4 2.9 + - - +
18L PHE* 5.3 9.9 - - + -
68L SER* 6.1 2.5 - - - -
108L CYS 4.2 0.8 - - - -
109L GLU* 1.3 71.6 - - - +
111L VAL* 1.3 72.2 + - - +
126L MET* 3.9 21.1 - - + -
127L ASP 3.2 5.6 - - - -
128L VAL* 4.2 4.7 - - + +
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Residues in contact with VAL 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L GLY 4.6 7.0 - - - +
13L GLN 3.9 10.1 - - - +
14L LYS* 4.0 14.8 - - + -
15L LEU* 4.7 0.2 - - - -
109L GLU* 4.8 7.9 - - + +
110L ALA* 1.3 86.6 - - - +
112L VAL* 1.3 59.9 + - - +
113L ALA* 2.5 31.5 + - + +
126L MET* 3.3 4.1 - - - +
127L ASP* 2.8 35.1 + - + +
129L TYR* 5.7 6.3 - - + -
160L LYS* 5.9 1.3 - - - +
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Residues in contact with VAL 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L GLY* 3.8 27.9 + - - +
13L GLN 3.3 17.6 + - - +
15L LEU* 3.7 25.8 - - + -
111L VAL* 1.3 72.1 - - - +
113L ALA* 1.3 61.7 + - - +
114L ASP* 2.8 19.5 + - - +
115L VAL* 3.8 13.9 - - + -
124L ILE* 3.5 39.0 - - + -
125L ILE 3.7 4.0 - - - -
126L MET* 4.4 3.4 - - + +
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Residues in contact with ALA 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L GLY 5.5 1.3 + - - -
111L VAL* 2.5 20.1 + - + +
112L VAL* 1.3 70.5 - - - +
114L ASP* 1.3 66.5 + - - +
125L ILE* 2.9 16.3 + - + +
127L ASP* 3.1 30.3 - - + +
160L LYS* 3.0 46.0 - - + +
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Residues in contact with ASP 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L GLY 5.7 2.7 - - - +
112L VAL* 2.8 7.1 + - - +
113L ALA* 1.3 79.3 - - - +
115L VAL* 1.3 94.5 + - - +
116L LEU* 4.3 0.4 - - - +
124L ILE* 3.6 0.7 - - - -
125L ILE* 2.9 40.0 + - + +
155L LYS* 3.3 27.7 + - - -
158L SER* 3.2 22.9 + - - +
159L ASP 5.4 0.2 + - - -
160L LYS* 3.3 24.1 - - + +
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Residues in contact with VAL 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L VAL* 3.8 19.1 - - + -
114L ASP* 1.3 99.2 + - - +
116L LEU* 1.3 71.0 + - - +
122L VAL* 3.2 29.6 - - + -
123L VAL 3.1 8.3 - - - +
124L ILE* 4.5 7.9 - - + -
125L ILE* 4.9 0.9 - - - +
152L PHE* 3.6 21.5 - - + -
155L LYS* 4.0 6.4 - - - +
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Residues in contact with LEU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L ASP* 4.3 1.3 - - - +
115L VAL* 1.3 84.0 - - - +
117L ASP* 1.3 63.3 + - - +
118L LYS* 4.4 18.6 - - - +
122L VAL* 2.8 9.4 - - - +
123L VAL* 2.6 60.7 + - + +
125L ILE* 5.2 6.7 - - + -
152L PHE* 4.2 3.1 - - - -
155L LYS* 4.0 18.6 - - + +
156L ARG* 4.3 20.2 - - - +
157L THR* 3.4 27.6 - - - +
158L SER* 4.0 15.0 - - - -
161L VAL* 5.7 2.5 - - + -
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Residues in contact with ASP 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 1.3 74.9 - - - +
118L LYS* 1.3 88.9 + - - +
119L GLY* 3.0 20.9 + - - +
121L GLY 3.6 7.4 - - - +
122L VAL* 4.4 2.0 - - - -
151L GLY* 3.3 16.3 + - - -
152L PHE* 2.4 49.3 - - + +
153L GLY 4.1 16.1 - - - +
154L GLY* 5.5 0.2 - - - -
155L LYS 4.6 13.5 + - - +
156L ARG* 5.7 2.1 - - - +
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Residues in contact with LYS 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 4.0 15.8 + - - +
117L ASP* 1.3 85.9 + - - +
119L GLY* 1.3 51.3 + - - +
120L SER* 2.7 21.1 + - - -
121L GLY 3.1 14.5 + - - +
123L VAL* 3.7 32.3 - - + -
145L PHE* 3.9 13.6 - - + -
156L ARG 4.5 12.9 + - - -
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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
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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