Contacts of the strand formed by residues 136 - 146 (chain I) 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 LEU 136 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97I TYR* 3.8 49.7 - - + +
98I LYS* 4.6 8.1 - - - +
129I TYR* 3.8 31.0 - - + -
130I SER 3.5 16.8 - - - +
131I TYR* 3.4 35.1 - - + +
135I GLU* 1.3 73.5 - - - +
137I ILE* 1.3 61.0 + - - +
138I CYS 3.8 9.0 - - - +
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Residues in contact with ILE 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I LEU* 3.6 0.9 - - - -
97I TYR* 2.7 35.5 + - - +
98I LYS* 3.3 33.3 + - + +
99I PRO 4.9 2.0 - - - +
100I LEU* 3.7 23.8 - - + -
101I PRO* 4.7 14.4 - - + -
106I LEU* 3.7 18.6 - - + -
130I SER* 2.8 16.8 + - - +
132I SER* 3.4 28.7 - - - +
135I GLU* 3.4 18.2 - - + +
136I LEU* 1.3 74.2 - - - +
138I CYS* 1.3 55.3 + - + +
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Residues in contact with CYS 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I GLY* 4.4 8.7 - - - -
64I ILE* 4.6 6.7 - - - -
94I LEU* 4.2 3.4 - - + -
95I GLU 3.3 12.3 - - - +
96I LEU* 3.8 18.2 - - + -
97I TYR* 4.0 4.3 - - - -
100I LEU* 4.5 13.7 - - - -
106I LEU* 5.8 0.4 - - - -
128I VAL 4.1 0.3 - - - +
129I TYR* 3.7 2.3 - - - -
130I SER* 3.0 50.0 + - - +
136I LEU* 3.8 3.7 - - - +
137I ILE* 1.3 84.6 - - + +
139I HIS* 1.3 61.8 + - - +
140I ASN* 4.3 13.7 - - - -
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Residues in contact with HIS 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I TYR* 3.8 20.7 - + - +
94I LEU* 3.3 4.7 - - - +
95I GLU* 2.9 34.3 + - + +
97I TYR* 3.6 28.7 + - + +
127I ASP* 2.6 32.2 + - - +
128I VAL 3.7 9.0 - - - -
129I TYR* 3.7 35.9 + + + -
138I CYS* 1.3 75.1 - - - +
140I ASN* 1.3 90.2 + - - +
141I GLN* 4.6 6.3 - - + -
162I LYS* 4.8 11.5 - - - -
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Residues in contact with ASN 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I GLY 2.9 22.9 + - - -
62I VAL* 3.3 11.4 - - - -
65I GLY* 3.8 14.1 - - - +
92I GLN* 3.3 16.5 + - - +
93I TYR 3.3 2.7 - - - +
94I LEU* 3.2 24.2 - - - +
127I ASP* 3.4 0.5 - - - -
128I VAL* 2.8 42.1 + - + +
130I SER* 4.8 0.6 + - - -
138I CYS* 4.3 8.5 - - - -
139I HIS* 1.3 80.0 - - - +
141I GLN* 1.3 59.4 + - - +
142I PHE* 3.4 25.8 - - + -
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Residues in contact with GLN 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I GLU 4.3 0.3 - - - +
92I GLN* 3.8 2.7 - - - -
93I TYR* 2.8 45.6 + - + +
125I ILE* 3.6 24.7 - - + +
126I MET 3.5 3.1 - - - +
127I ASP* 2.8 27.5 + - - +
139I HIS* 4.2 4.7 - - - +
140I ASN* 1.3 73.0 - - - +
142I PHE* 1.3 61.2 + - - +
143I SER* 3.7 6.4 + - - -
160I LYS 2.9 27.9 + - - -
161I VAL* 3.2 30.1 - - - +
162I LYS* 3.4 18.6 + - - +
243I LYS* 4.8 5.4 + - - -
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Residues in contact with PHE 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I VAL* 3.6 17.5 - - + -
65I GLY 3.6 6.3 - - - -
66I GLN* 3.5 28.9 - - + -
68I SER* 5.8 0.4 - - - -
69I MET* 3.3 43.7 - - + -
89I HIS* 4.0 1.6 - + - +
91I GLU 4.1 0.2 - - - -
92I GLN* 3.0 31.2 - - - -
124I ILE 3.7 2.3 - - - +
125I ILE* 3.7 1.4 - - - +
126I MET* 3.0 39.6 + - + +
128I VAL* 3.5 22.2 - - + -
140I ASN* 3.4 23.8 - - + -
141I GLN* 1.3 71.4 - - - +
143I SER* 1.3 59.9 + - - +
144I LEU* 3.7 15.7 + - + +
217I LEU* 4.5 1.3 - - + -
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Residues in contact with SER 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I HIS* 3.7 2.1 - - - -
90I GLY* 2.7 33.3 + - - -
91I GLU* 3.0 49.7 + - - +
123I VAL* 3.7 18.5 - - - +
124I ILE 3.9 4.3 - - - -
125I ILE* 4.7 11.7 - - - +
141I GLN* 3.7 6.4 + - - -
142I PHE* 1.3 71.6 - - - +
144I LEU* 1.3 53.5 + - - +
161I VAL* 6.0 1.1 - - - -
243I LYS* 5.4 1.6 - - - -
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Residues in contact with LEU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I MET* 3.7 35.9 - - + +
74I LEU* 3.2 35.7 - - + -
87I VAL* 3.9 17.7 - - + -
88I LEU 3.2 12.6 - - - +
89I HIS* 4.1 12.6 - - + -
122I VAL 3.9 0.2 - - - +
123I VAL* 3.3 8.9 - - - +
124I ILE* 2.9 50.2 + - + +
126I MET* 5.2 4.0 - - + -
142I PHE* 4.2 13.9 - - + +
143I SER* 1.3 79.0 - - - +
145I PHE* 1.3 60.7 + - - +
146I LEU* 4.2 1.8 - - + -
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Residues in contact with PHE 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I LYS 3.3 2.4 - - - +
88I LEU* 2.5 57.4 + - + +
90I GLY* 4.9 9.2 - - - +
118I LYS* 4.0 26.5 - - + -
120I SER* 5.0 5.2 - - - -
121I GLY* 3.7 25.4 - - - -
122I VAL 3.6 2.7 - - - -
123I VAL* 4.0 17.7 - - + -
144I LEU* 1.3 74.3 - - - +
146I LEU* 1.3 75.1 - - - +
147I VAL* 4.1 17.7 - - + -
148I GLY 5.1 0.2 - - - -
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Residues in contact with LEU 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I PHE* 4.3 12.1 - - + -
74I LEU* 6.3 0.2 - - + -
82I ILE* 3.5 39.9 - - + -
83I ASN 5.2 0.7 - - - +
86I LYS* 3.3 7.0 - - + +
87I VAL* 3.6 31.4 - - + -
121I GLY* 3.1 21.5 - - - -
122I VAL* 3.0 13.7 + - + +
124I ILE* 3.8 31.4 - - + -
145I PHE* 1.3 74.8 - - - +
147I VAL* 1.3 66.2 + - - +
149I SER* 4.0 26.1 + - - +
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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