Contacts of the helix formed by residues 103 - 118 (chain A) in PDB entry 4RTP
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 ASP 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 5.5 1.0 + - - -
101A SER* 3.2 3.9 + - - +
102A GLN* 1.3 76.6 - - - +
104A PRO* 1.3 68.2 - - - +
105A PHE* 3.5 16.1 + - - +
106A ARG* 3.0 32.1 + - + +
107A ARG* 2.9 33.7 + - - +
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Residues in contact with PRO 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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61A SER* 4.2 19.9 + - - +
65A ILE* 4.2 14.2 - - + +
69A ARG* 6.2 0.2 - - - +
102A GLN 3.3 9.6 - - - +
103A ASP* 1.3 93.8 - - - +
105A PHE* 1.3 55.7 + - - +
107A ARG* 3.5 9.0 + - + +
108A ALA* 2.9 30.4 + - - +
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Residues in contact with PHE 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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65A ILE* 3.8 20.8 - - + +
69A ARG* 3.6 38.5 - - - +
72A GLU* 3.6 45.8 - - + -
73A TYR* 3.7 27.6 - + + -
76A ALA* 3.9 12.3 - - + -
103A ASP* 3.3 15.4 + - - +
104A PRO* 1.3 79.0 - - - +
106A ARG* 1.3 61.7 + - - +
108A ALA* 3.2 4.9 + - - +
109A VAL* 3.0 46.6 + - + +
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Residues in contact with ARG 106 (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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76A ALA* 5.5 2.4 + - - +
80A LEU* 4.5 9.3 - - - +
94A PHE* 3.7 18.0 - - - -
97A GLU* 2.7 41.1 + - + +
101A SER* 3.8 15.0 - - - +
103A ASP* 3.0 26.5 + - + +
105A PHE* 1.3 81.8 - - + +
107A ARG* 1.3 57.0 + - - +
109A VAL* 3.3 22.2 + - - +
110A LEU* 3.0 45.0 + - + +
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Residues in contact with ARG 107 (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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58A ASP* 2.9 31.1 + - - -
98A PHE* 2.8 64.2 + - + +
99A ASN* 4.2 9.9 + - - +
101A SER* 3.5 35.8 + - - -
102A GLN 4.8 1.6 - - - -
103A ASP 2.9 23.7 + - - +
104A PRO* 3.8 7.9 - - + +
106A ARG* 1.3 75.7 - - - +
108A ALA* 1.3 58.1 + - - +
110A LEU* 3.4 1.3 + - - -
111A PHE* 2.8 31.2 + - - +
125A TYR* 5.8 0.2 - - - -
129A GLY 5.5 4.2 + - - -
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Residues in contact with ALA 108 (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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58A ASP 6.0 0.2 - - - -
61A SER* 5.2 0.7 - - - +
62A LEU* 3.5 26.4 - - + +
65A ILE* 4.0 19.5 - - + -
73A TYR* 2.7 34.6 + - + -
104A PRO 2.9 19.0 + - - +
105A PHE 3.2 5.4 + - - +
107A ARG* 1.3 73.9 - - - +
109A VAL* 1.3 62.0 + - - +
111A PHE* 3.5 10.6 + - - +
112A LEU 3.5 4.7 + - - -
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Residues in contact with VAL 109 (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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73A TYR* 3.6 23.6 - - + -
76A ALA* 3.9 15.9 - - + +
77A ALA* 3.8 21.1 - - - +
80A LEU* 3.7 25.6 - - + +
81A PHE* 5.6 0.5 - - - -
105A PHE* 3.0 38.3 + - + +
106A ARG* 3.5 20.9 - - - +
107A ARG 3.3 0.2 - - - -
108A ALA* 1.3 79.7 - - - +
110A LEU* 1.3 61.8 + - - +
112A LEU* 3.4 11.3 + - - +
113A TYR 3.5 7.4 + - - -
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Residues in contact with LEU 110 (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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80A LEU* 3.7 20.2 - - + -
94A PHE* 3.6 38.1 - - + +
97A GLU* 3.7 20.2 - - + +
98A PHE* 3.6 42.2 - - + +
101A SER* 5.2 0.4 - - - -
106A ARG* 3.0 39.9 + - + +
107A ARG* 4.0 3.4 - - - +
109A VAL* 1.3 74.4 - - - +
111A PHE* 1.3 59.3 + - - +
113A TYR* 3.1 3.8 + - + +
114A LEU* 2.9 34.9 + - + +
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Residues in contact with PHE 111 (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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8A LEU* 4.6 9.6 - - + -
10A TRP* 4.1 22.0 - + - -
58A ASP* 3.6 25.6 - - + +
59A LEU* 4.5 10.1 - - - -
62A LEU* 3.6 27.4 - - + -
98A PHE* 3.6 25.4 - + + -
107A ARG 2.8 18.2 + - - +
108A ALA* 3.6 10.8 - - - +
109A VAL 3.2 0.2 - - - -
110A LEU* 1.3 78.4 - - - +
112A LEU* 1.3 56.3 + - - +
114A LEU* 3.9 6.3 - - + +
115A ASN* 3.0 32.4 + - + +
123A CYS* 4.0 20.2 - - - -
125A TYR* 3.8 11.4 - + - -
131A PHE* 5.0 8.5 - + - -
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Residues in contact with LEU 112 (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 PHE* 3.8 21.8 - - + +
8A LEU* 3.7 25.8 - - + -
62A LEU* 5.3 1.5 - - + +
73A TYR* 3.3 27.6 - - + +
77A ALA* 4.3 4.7 - - + -
81A PHE* 3.7 10.9 - - + -
108A ALA 3.5 1.8 + - - -
109A VAL 3.4 5.7 + - - +
110A LEU 3.2 0.2 - - - -
111A PHE* 1.3 76.6 - - - +
113A TYR* 1.3 65.5 + - - +
115A ASN* 3.4 2.9 + - - +
116A ARG* 3.2 30.7 + - + +
143A PHE* 4.2 16.8 - - + -
144A PRO* 4.3 8.1 - - + -
148A LEU* 3.9 29.8 - - + -
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Residues in contact with TYR 113 (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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80A LEU* 3.6 39.9 - - + -
81A PHE* 4.0 10.4 - + + -
85A THR* 2.6 42.3 + - - -
90A VAL* 4.1 0.2 - - - +
91A TYR* 3.4 40.9 + + - +
94A PHE* 3.6 37.5 - + + -
109A VAL 3.5 2.6 + - - -
110A LEU* 3.1 7.8 + - + +
112A LEU* 1.3 78.9 - - - +
114A LEU* 1.3 65.0 + - + +
116A ARG 3.2 1.4 + - - -
117A TYR* 2.8 68.5 + + + +
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Residues in contact with LEU 114 (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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91A TYR* 3.7 29.2 + - + +
94A PHE 5.0 0.2 - - - +
95A ARG* 3.8 31.2 - - + +
98A PHE* 3.7 44.2 - - + -
110A LEU* 2.9 19.5 + - + +
111A PHE* 3.9 7.6 - - + +
113A TYR* 1.3 86.1 - - + +
115A ASN* 1.3 57.0 + - - +
118A GLY* 2.9 28.9 + - - -
121A GLY* 5.6 0.2 - - - -
122A LEU 5.2 1.4 - - - +
131A PHE* 3.9 32.0 - - + -
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Residues in contact with ASN 115 (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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8A LEU* 3.6 20.7 - - + +
9A LYS* 2.7 55.4 + - - +
10A TRP* 4.2 13.1 - - - -
111A PHE* 3.0 23.4 + - + +
112A LEU 3.7 5.2 - - - +
113A TYR 3.2 0.2 - - - -
114A LEU* 1.3 77.4 - - - +
116A ARG* 1.3 65.8 + - - +
118A GLY 4.5 0.5 + - - +
121A GLY* 3.4 33.2 + - - -
122A LEU 5.0 5.8 + - - -
123A CYS* 5.8 0.6 - - - +
131A PHE* 5.3 1.3 - - - -
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Residues in contact with ARG 116 (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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6A ALA 4.0 6.9 + - - -
7A PHE* 3.0 36.4 + - - +
8A LEU 3.9 7.5 - - - +
9A LYS* 3.7 45.3 + - - +
81A PHE* 3.6 28.0 - - + -
112A LEU* 3.2 21.9 + - + +
113A TYR 3.2 0.9 + - - +
115A ASN* 1.3 87.8 + - - +
117A TYR* 1.3 63.0 + - + +
118A GLY 3.6 0.7 - - - -
138A TYR* 3.7 6.8 - - - -
141A PRO* 3.7 15.4 - - + +
142A TYR* 3.5 38.5 + - - +
144A PRO* 4.3 9.4 - - + +
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Residues in contact with TYR 117 (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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81A PHE* 3.4 41.6 - + - +
82A VAL 3.8 6.6 + - - -
85A THR* 3.6 18.8 + - - -
86A ASN* 3.6 37.6 - - + +
91A TYR* 3.9 17.7 - - + -
113A TYR* 2.8 44.4 + + + +
116A ARG* 1.3 81.7 - - + +
118A GLY* 1.3 62.4 + - - +
135A PHE* 3.7 11.1 - + + -
136A GLY* 2.8 25.3 + - - -
137A ARG 4.0 0.9 + - - -
138A TYR* 4.2 5.5 - - - -
141A PRO* 3.5 34.7 + - + +
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Residues in contact with GLY 118 (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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91A TYR* 3.4 19.9 - - - -
114A LEU 2.9 21.1 + - - -
115A ASN 4.5 0.7 - - - +
116A ARG 3.6 0.2 - - - -
117A TYR* 1.3 79.7 + - - +
119A TYR* 1.3 63.6 + - - -
120A ASN 3.3 0.9 + - - -
121A GLY* 3.4 10.4 + - - -
122A LEU 6.0 0.4 - - - -
133A VAL* 4.3 3.8 - - - -
134A PRO 3.7 2.2 - - - -
136A GLY* 3.7 1.1 - - - -
138A TYR* 3.2 17.7 - - - -
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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