Contacts of the strand formed by residues 139 - 150 (chain H) in PDB entry 6C6S
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 SER 139 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62H ASP* 4.2 8.8 - - - +
71H LYS* 5.4 4.3 - - - +
103H ASN* 6.0 0.3 - - - +
104H LYS 3.3 8.0 + - - -
105H SER* 3.7 15.6 - - - -
137H ASN 3.2 9.2 + - - -
138H ALA* 1.3 72.3 - - - +
140H ILE* 1.3 69.8 + - - +
141H SER* 4.0 1.7 + - - -
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Residues in contact with ILE 140 (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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61H ILE* 5.2 7.4 - - + -
62H ASP* 4.9 0.7 - - - +
71H LYS* 4.8 14.8 - - + -
74H VAL* 4.5 21.8 - - + -
81H ILE* 5.4 2.7 - - + -
102H LEU* 4.4 13.0 - - + +
103H ASN* 3.4 9.0 - - - +
104H LYS* 2.5 50.9 + - + +
110H VAL* 5.0 10.1 - - + -
131H CYS* 5.3 8.5 - - - -
133H LEU* 4.8 12.1 - - + -
138H ALA 4.0 0.8 + - - -
139H SER* 1.3 79.8 + - - +
141H SER* 1.3 68.2 + - - +
142H MET* 3.7 27.8 - - + -
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Residues in contact with SER 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ILE* 4.1 1.2 - - - +
62H ASP* 3.1 51.4 + - - +
101H THR* 5.2 1.4 + - - -
102H LEU 3.3 6.5 - - - -
103H ASN* 3.0 14.1 + - - -
139H SER* 5.1 1.3 - - - -
140H ILE* 1.3 81.1 - - - +
142H MET* 1.3 61.6 + - - +
143H ARG* 5.9 1.6 - - - +
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Residues in contact with MET 142 (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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59H VAL* 4.6 4.3 - - + -
60H GLU 3.7 4.5 - - - -
61H ILE* 3.7 26.7 - - + -
81H ILE* 3.8 26.5 - - + -
85H LEU* 4.5 27.4 - - - -
101H THR* 3.0 5.8 + - - -
102H LEU* 2.9 67.7 + - + +
130H ILE* 4.9 2.9 - - + -
131H CYS* 5.4 1.8 - - - -
140H ILE* 3.7 27.1 - - + -
141H SER* 1.3 75.8 - - - +
143H ARG* 1.3 63.7 + - - +
144H ILE* 4.2 6.7 + - + -
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Residues in contact with ARG 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLU 4.3 0.3 - - - +
59H VAL* 3.3 5.0 - - - +
60H GLU* 2.8 70.0 + - + +
99H ILE* 4.7 20.3 - - + +
100H LEU 3.4 7.2 - - - +
101H THR* 4.1 19.6 + - - +
141H SER* 5.9 2.0 - - - +
142H MET* 1.3 77.6 - - - +
144H ILE* 1.3 60.3 + - - +
145H LYS 4.3 0.4 + - - -
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Residues in contact with ILE 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H VAL* 3.7 39.7 - - + -
58H GLU 4.1 1.8 - - - -
59H VAL* 3.9 10.1 - - + -
85H LEU* 3.8 26.5 - - + -
88H LEU* 4.2 11.7 - - + -
99H ILE* 4.7 1.5 - - - +
100H LEU* 2.6 66.9 + - + +
101H THR* 4.1 8.3 - - - +
102H LEU* 5.1 3.6 - - + +
115H ILE* 5.3 10.3 - - + -
142H MET* 4.8 9.2 - - + +
143H ARG* 1.3 75.0 - - - +
145H LYS* 1.3 60.0 + - - +
146H VAL* 3.9 5.5 + - + -
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Residues in contact with LYS 145 (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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56H VAL* 3.8 2.0 - - - +
57H THR* 2.8 25.9 + - - -
58H GLU* 3.0 53.1 + - + +
97H GLU* 3.4 37.6 + - - -
98H VAL 3.9 12.1 - - - +
99H ILE* 4.3 14.1 - - + +
143H ARG 4.3 0.4 - - - -
144H ILE* 1.3 72.6 - - - +
146H VAL* 1.3 73.2 + - - +
147H GLN* 4.5 9.9 + - - +
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Residues in contact with VAL 146 (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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54H CYS* 5.3 2.0 - - + -
55H ALA 3.3 12.3 - - - +
56H VAL* 4.0 24.9 - - + +
88H LEU* 6.2 0.4 - - + -
90H VAL* 4.4 20.0 - - + -
92H VAL* 4.3 17.3 - - + -
97H GLU* 3.7 2.3 - - - +
98H VAL* 3.2 50.5 + - + +
100H LEU* 4.0 16.6 - - + -
121H VAL* 4.7 0.2 - - + -
144H ILE* 3.9 6.6 + - + -
145H LYS* 1.3 82.8 - - - +
147H GLN* 1.3 65.1 + - - +
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Residues in contact with GLN 147 (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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54H CYS* 4.1 3.3 - - - +
55H ALA 2.9 28.4 + - - +
57H THR* 3.3 32.4 - - - +
96H ASP* 4.2 2.2 - - - +
97H GLU* 3.2 33.5 + - + +
145H LYS* 4.5 7.8 + - - +
146H VAL* 1.3 79.2 - - - +
148H ARG* 1.3 74.9 + - - +
158H ARG* 4.3 7.0 + - - +
177H TYR* 3.3 15.1 + - + -
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Residues in contact with ARG 148 (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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52H PRO* 5.2 8.8 - - + +
53H GLY* 3.4 27.3 - - - +
54H CYS* 3.5 22.1 - - - +
92H VAL 2.4 33.5 + - - +
93H GLN 3.4 13.3 + - - -
94H GLY* 5.4 0.6 - - - -
95H LYS 4.2 6.7 + - - -
96H ASP* 3.3 36.5 + - - +
147H GLN* 1.3 87.8 + - - +
149H GLY* 1.3 64.2 + - - +
177H TYR* 4.0 1.9 - - - -
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Residues in contact with GLY 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H PRO* 3.3 6.9 - - - +
53H GLY 2.8 28.7 + - - -
148H ARG* 1.3 78.1 - - - +
150H ARG* 1.3 64.9 + - - +
177H TYR* 3.4 23.6 - - - -
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Residues in contact with ARG 150 (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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7G GLU 2.5 44.5 + - - +
8G PHE* 3.3 31.2 - - + -
32G GLU* 2.5 34.6 + - - +
33G ARG* 5.7 2.4 + - - -
195G ARG* 5.2 8.4 - - - +
49H SER 3.0 13.9 - - - +
50H SER* 3.7 8.1 - - - -
51H MET 3.4 11.9 - - - +
52H PRO* 5.2 3.8 - - + -
149H GLY* 1.3 78.2 - - - +
151H GLY* 1.3 59.3 + - - +
152H TYR 4.0 1.2 + - - -
153H VAL* 6.5 0.4 - - - -
177H TYR* 3.6 6.3 - - - -
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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